It’s not a question of making iso. It’s a question of not spending iso.
If you just try to maximum level everything, you’re going to be short on iso. That’s how it works (well usually anyways). You can play Lightning Rounds for more iso, but as you’re already doing PvE and PvP your iso income is pretty well capped so you need to observe austerity measures.
As to where you shouldn’t spend iso - well it’s a matter of priorities.
As I see it, Rocket and Groot is a big 4* to use in terms of cutting real times in PvE. Medusa is also pretty strong when combined with Carnage (particularly, cuts down on health pack usage). Vulture and America Chavez can be used to good effect, and though I don’t care for Ghost, she’s not bad.
BUT - the question is, where do you really need iso?
You don’t need to push iso into your 3*s. Yes, eventually you do, then you champ then get rewards, but you don’t really have the iso so much right now. You can save covers and not champ for now, deferring those rewards for later when you have the iso.
Probably you will want to keep your 2* farms going. You are losing iso by rotating through your 2* farms, but you are gaining tokens, HP, and covers that help your development overall. Plus you are generating a lot of tokens what with your good placement in PvP and PvE. You could technically save iso and save covers, but in practice I don’t know that would work so well - 2*s don’t require that much iso, and trying to juggle them is just more trouble than it’s probably worth - though if you’re really up for austerity, you could think on it.
But really if you’re having trouble with your 2* farms - it’s probably because you’re pushing your 4*s to 240. They don’t need to be at 240. 209 is fine. 240 you get a performance boost sure, but you don’t need it so much. See what I mean?
The last few levels on a 4* cost a lot more than the first few levels, and each additional single level doesn’t make that much dfiference. So do you really need to push iso into assorted 4s? I’d say no. Think about the 4s you really use a lot, and put iso into them only. And if it’s more than two or three, well, you don’t really have the iso to be pushing iso into trying to champ more. So you have to not-spend somewhere. See?
Mind I think if you push iso into 4s you will probably increase your MMR in PvP, but that’s as it goes. (You do know what I mean?) Putting iso into those 4s can help you cut times in PvE at least, assuming you’re playing at SCL 7 or whatnot.
However . . .
You already have iso in most of your more covered 4s. So I think you’ll probably already be able to use them to cut times in PvE. So at this point I would think instead of spending iso, maybe you just want to sit on iso and not use it. Then if a particular 4 comes up in Deadpool Daily Crash of the Titans or SHIELD training, you have the iso to level it to 209 - which I notice you stopped some 4*s at already, probably because you already know 209’s where you need to be to get all the rewards off SHIELD training but mentioning it here again just to be sure.
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That is - I’d say generally try to keep a bank of iso so you have to spend when you need it. I don’t think you need to push iso into championing your 3* what with saved covers (you should do it eventually certainly but I don’t think there’s a rush). Your 4*s are mostly developed, but apart from maybe championing Medusa to switch her to 5 yellow covers, Carnage is already going to be okay I think because his function is to generate Specials which he already does at his current covers You might push Chavez too, but apart from that I don’t know that I’d say anything is terribly urgent - maybe Iceman, or whoever you really plan to use.
But again, try not to spend if you can help it. Think about what you REALLY need, and remember you can save covers. I know you probably want to get on with championing and get it over with, but really you just don’t have the iso, and apart from buying it in the store (which I think many would recommend against, it costs a lot to get enough iso to make a difference), the only way to get more iso is to just not spend it.