It would be nice to see some upgrades for bainar, maybe something like this:

Bainar II Systems Upgrade
Upgrades a Bainar, Systems Cracker ally, reducing the ability timer by 1 hour(to 1 day 15 hours) and increasing its hack bonus to +16%.
Requires Rank 500 or Greater.
Requires: 1200 Medal Points Earned
Cost: 500 blue badges

Upgrades could go until Bainar V(i think 4 upgrades is ok, would be happy with more obviously), ability timer would drop to 36 hours(minor drop from 40) and hack bonus would be at +19%, not as pretty as +20% but I can deal with that.
The requirements for each upgrade could go up, maybe by 100s(upgrade 3: rank 600+, 1300 medal points, 600 blues etc)
Maybe give out medals for each upgrade(10 points).

Bainar/Timer/Hack Bonus
1/40/15%
2/39/16%
3/38/17%
4/37/18%
5/36/19%

Honestly, I just want to see something new, even if it is just an upgrade to something that already exists(and want a lower timer for the ability ).

I'm for it, especially for something that is non-GP related. We've seen upgrades for Thraccti and Cuniculus which ARE Gp related, so why not something that isn't? I'd add in to the final upgrade of him: Allows your Bainar PRIME (+3) structures to be upgraded, adding 1 to their existing production, whatever type that may be. Make it cost something like 20-30 blue badges if that isn't too high, especially since blues are easy to get. I would make only the Primes upgrade-able because then that would at least not diminish the randomness of bainar. It would give another 1:4 artifact structure in our existing pool of them, which are only acquired ultimately through GP. It might be nice to have one that is attainable through regular means.

That said with Bainar, I'd like to see upgrades to other non-GP allies too. I'd like to see even a mini-mission chain (like 3 missions maybe?) dealing with Vortov and the Bralkir faction - A chain that could upgrade him somewhere in, allowing him to see an additional NPC variety.

+1 Very neat idea, upgrading the Ally unlocks additional items in the battle market (bought with blues) that can upgrade his structures. Has the added benefit of discouraging random TIB spamming because everyone with Jam Attenuator has a massive stockpile of blues and what else ya gonna do with them?