How do CNDRs become obsolete? They are the same strength as Disciples and are not obsolete until you get to Sup 11 and may even get their promotion before the Disciples do if you pick up a few Harmony or Purity levels.
I also don't 'rush' to Sup 11 as I often pick up a few side techs here and there. In fact my tech path more often than not promotes the CNDRs to True before I get T3 marines so that pack of True CNDRs is ready much earlier, and they see more battle so they are higher level.
I think making the Affinity units stronger compounds the problem already complained very much about, the narrow tech path to victory caused by the victory conditions. Making them OP forces the player to b-line for level 13 as they get super units as the double bonus.
Your upgraded marines are going to have 2 perks that your CNDRs/battlesuits/xeno swarms do not have, immediately making them stronger than the unique units. Again, given you can start building them from the word go for cheaper there's really no reason not to spam them instead of waiting on unique units who are going to be inferior within a few dozen turns at most while sucking up your strategic resources.
The issue with making affinity units stronger, to my line of thinking, is not so much it encourages beelining techs (that's going to happen anyway with the current system where affinity is tied to science, and science is the only non-domination victory path for all intents and purposes) but that they don't have a good limiting factor in the game right now. Simply put strategic resources are too abundant and easy to come by for that to be an issue, especially with the game favouring sprawl. The design of the units doesn't help either. CNDRs are supposed to be this crazy strong defensive unit that's bad at going on the offensive but that's just fluff written in the encyclopaedia, and not something that actually exists in game terms to stop you from building a bunch of them and taking cities if you want to. Battlesuits are supposed to be some elite unit of very experienced troops who are presumably limited in number, but in game terms that never manifests as you can build as many as you have titanium for. Xeno swarms... well whatever they're xeno swarms, those I actually don't have much of a problem with as they more or less fill their role as cheap, expendable horde units although I feel they could be a little cheaper or a little stronger (or maybe both).
To my line of thinking there are two routes to take to buff CNDRs and battlesuits without reverting the game to launch state where you just spam your early affinity units and stomp everything in your path. One, add an artificial limiting factor to the game, whether that be by vastly increasing strategic resources required, or simply hard capping the number of the units the player can build one way or another. I dislike this option as, quite frankly, it feels lazy and unimaginative although it certainly could work. Two, add promotions that actually make the unit do what it's supposed to do in the fluff, while vastly increasing maintenance/production cost to discourage spamming the unit. So perhaps nerfing base combat strength of the CNDR while giving it a huge buff (like, 200-400% buff) to fighting near your cities/capital, or in your own territory so it actually fills it's role as a defensive unit might be a place to start, although I'd want to see an increase in maintenance cost so a player doesn't just spam the hell out of them and turtle/snipe cities and use them as super units. Makes the unit very useful in defending your territory, but stops the player from rushing them and going on a rampage. Battlesuits on the other hand could get a buff to their combat strength and promotions making them act kinda like tacnets/great generals in CiV, but also be made astronomically more expensive to build/maintain, while perhaps also having each battlesuit built make the the next battlesuit more expensive to build/purchase (kinda like national wonders increase in production based on number of cities in CiV) to keep the number of battlesuits on the field low. Just as an example of course, there are probably better ways to discourage spamming battlesuits, but that's the first idea that comes to my mind anyway. Something to see them be very useful to have on the field leading formations, but not making up the bulk of an army in general makes sense to me.
and I know you played that alot!
