TLDR: Make Joja cheaper, but have a % of all money spent buying Joja products go towards forcing you to become a Joja member. Exact mechanisms can very from that base.
Ooh, OP got a reply. Lucky. I was scrolling through Ape's other posts, and that seems to be the first suggestion thread post that I can see. Doesn't post much at all, other than replies to bugs and stuff. I would have thought there would be a few more. Honestly, if you want to keep adding to the game, it seems like you could spend another 5 years adding them. There is a lot of interesting stuff to talk about when discussing improvements to the game.
Anyway, inferior seeds does seem a bit complicated to manage. I personally don't like the idea of different quality seeds. Different quality seeds mean that the produce made will also be different as well. If you plant a joja blueberry seed, get the blueberry, and then make that blueberry a seed, then that seed will also have to be of the lower quality. Basically, you are adding a new item number for every single growable item that Jojo sells. Meh. You can do it, but I am not a fan of this method, and I don't think it adds much to the narrative. By making it lower quality, you are still making players want to buy from Pierre instead, and the goal is to make a player want to buy from Joja. You aren't really acting like the savior of the town if you are constantly buying there.
On the other hand, if it's better to buy from there, players are going to do so, so you need any savings to be minimal. You could add a lot of story elements, to try and guilt the player into doing the "right" thing, but that seems like a lot of work.
While I think it was a good call to not have a time limit on how long it takes to complete the game (there is no way I'm finishing the the fish bundles in the week I have left before end of year 2, and I would not have been happy to have my work wrecked because of that), I feel that this looming threat is what needs to be leaned into in order to make the player not want to buy from the mega-mart.
I'd suggest a flat 5% discount of Joja over Pierre's in everything until the community center question is resolved. You might ask if there is an increased saving after becoming a member. I'm going to say no, and that it will be less, in fact, but that I have an idea for this.
My idea is to add a mechanic that buying from Joja creates an in store credit that lowers the cost of the 5k membership. Yes, buying from Joja is cheaper, and helps you out personally, but doing so inches you closer to gaining that last membership needed to convince the mayor to sell the community center. This adds a bit of a ticking clock by getting something in the mail every time you pass another 1k spending milestone in Joja. Next day you get a letter from Joja saying that the Joja in-store credit program has added 100$ to the cost of becoming a full member (or a mail saying you got 200$ for spending 2k that day, and so on).
I would imagine the process would work like this. Joja works like one of those bulk membership stores. You cannot buy products unless becoming a member. With Joja, there is becoming part of the 5,000$ membership club, or being given a guest pass (cost is the same for a 'guest' as it is for a member, so no extra discount for "officially" joining). If you try to buy without being a member/guest, the cashier will say that you have to join first, and to please talk to the manager. When talking to the manager, he offers the full membership, and when you say no, he fast talks you into taking a guest pass. Afterwards, he tells you that you can also become a full member just by buying 50k worth of products from the store using your guest pass.
This would also answer the question of why did everyone else buy such an expensive membership in the first place. They didn't, the manager pulled the same trick on all of them, and they kept buying from the Joja until ending up getting the full membership as a result.
Also, you should get some mails advertising sale days, sales being the real draw that brought people to buy there. I'd say they could happen once a month or so. Could also just have them posted on the calendar as well. Alternatively, if you want to go with the coupon route. You get a letter, there is a coupon attachment, the attachment flies into your wallet, and stays there until you enter Joja. Afterwards, it triggers/disappears. Anything you buy in Joja that day is 1/2 off. However, buying on sale also increases the membership bonus as well. For every 1k you spend on a sale day, you get 200$ towards a new membership, instead of 100$. Minimum of 200$ bonus if you buy anything, even if you don't spend a full 1k that day. Sale days are counted separately from normal days, and do not stack with other sale days.
With a little additional work, you could do it for specific products as well. That backpack for 2k at Pierre's? The same day you get an advertisement from Pierre, you also get one from Joja, and Joja is actually open on Wednesday, the day you get the letter (no idea why that ad for the backpack comes on the day that Pierre's is closed). Furthermore, the Joja backpack is only 1k. If you buy from one, the other also disappears at the same time. Good deal, right?
The downside is that the Joja backpack is worth 5 times the normal amount of in-store credit towards becoming a full Joja member. So, you can buy that backpack for just 1k, but it puts you 500$ closer to that 5000$ membership. Not so bad, you think, but then you see that 10k second upgrade backpack at Pierre's is only 5k at Joja, so you buy that too, and now you are 500+2500=3k down the road to the full membership (could add an achievement saying something like "sold half my soul to Joja" after getting past the 2,500 mark as an additional mark of shame for buying too much there).
You promise not to buy anymore, but, wait, just after you sent your hoe to be upgraded to a copper hoe, there is a new flier that says you can trade in your old worn down tools to Joja, and get brand new upgraded ones for half the cost as at the local blacksmith, AND you don't need to give any ore, or wait 3 days? Normal cost for upgrading all four of your tools (trash can excluded) is 8k, plus 20 copper bars, and wait a total of 12 days. If you use Joja, you only have to spend 4k, give 0 copper bars, and wait 0 days. The one downside is that you have to buy all 4 tools as a package deal, and this includes the tool that you recently upgraded (this deal is triggered by buying your first copper tool. When you buy it, the deal to buy them all is posted the next day). That said, I'm still saving 3k overall. Plus, I don't have to wait 3 days or find more copper. While it's annoying to buy everything at once, it's still the better deal. So you do that. All good, right?
Not so much. See, that purchase was also a special deal. Which means it's at 5 times the normal in store credit rate. Lets see, 4k normally gives a return of 400. Times 5 and it's up to 2k. Meaning that you are adding another 2k to the full membership program. You were at 3k, after buying the two backpack upgrades, with another 2k... Oh, it seems you bought enough that you are now a full member. Bye, bye, Community Center.
This is how I'd envision Joja working. With 3 simple purchases, you can instantly get sucked in, and they are all so very tempting purchases to make, but if you have a strong will, and don't allow yourself to sell your soul to Joja, you can became a true savior of Pelican Town. This tool idea gets more tempting as time goes on. Iridium tools for half off, and no more mining? Ugh, but doing that would instantly mean you became a Joja member. You can't do it. On the other hand, you can skip that grinding....
Now, here is the fun part, as soon as Joja gets the community center (or maybe after all the community upgrades are purchased), there will be one last letter sent out to the player (and town). Something along the lines of Joja being unable to keep giving the low, low, prices of the past due to the expense of buying the community center, or some such nonsense. From now on, Joja customers will now pay 5% more than at Pierres. Joja doesn't care anymore. It got what it wanted.
Additionally, you could cap the number of items Pierre sells at a monthly limit at this point, which shows how he's being squeezed out. If you want to buy more than 500 blueberries during summer, then you need to get the rest at Joja. Maybe the Joja manager is now selling items at the various festivals, instead of Pierre, as well, and there are no more sales. Add some new dialogue for the wife to explain why Joja is selling instead of Pierre, and Pierre doesn't bother coming out for those events anymore. Not needed, but it sells that Joja is in charge of the town now.
Also, keep note that the cost for directly buying a a full membership also goes down as you buy more. It was initially 5000$, but a year later on, after making several Joja purchases, you talk to him again, and find out that it now only cost 3400$. Talking to the manager is also the only way to find out how close you are to becoming a full member as well.
This gives a fun push/pull to the threat of Joja but it's also easy to avoid as well. I've played almost 100 hours in my new playthrough, and I haven't bought a single thing from Joja. I might have, however, if I got some mail offering sweet deals, and a competitive price point, even if that would start me on the path to becoming a full member.
This seems a fairly simple option to add, in my mind. Most of it doesn't require anything all that is new. A bit of dialogue added when you first talk to the Joja manager, some mail from time to time, a message telling you that you need to be a member to buy anything, and a tracker for how much money you spent at Joja, and you gain the membership for free. If you want to go with the special items idea, which would count separately from the normal purchase/sales, just add a display area to buy separately, like with the backpack. The tool idea would need you to carry all 4 tools with you and they are all traded in for the new ones.
I'm no programmer, or even a modder, but I think this would be easy enough to implement. Most importantly, I feel this makes Joja the actual threat the game says they are, and plays well with the themes of the game.
PS. On another note. Apperently you can become a member before getting the cutscene of the mayor talking about the community center? Not sure if that was fixed or not, but there is no reason for that cutscene to trigger if you became a member first.