Regarding SEK removal, that seems off.
I feel like if you are removing it from some bundles, you should probably remove it from all of them, since as you mentioned earlier, SEKs are used to promote cooperation between bundle users and it doesn't make sense for some bundles to retain SEKs and some to not get them.
I do agree that SEKs are quite hit and miss though - they are useful when Syndicate Research Base is manned and you have someone watching your back, but otherwise it is underwhelming. That is kind of outside the purview of this thread though I believe.
Some other points I would like to raise:
Krav Maga on Infilitrator seems a bit weird, considering the intent is to jump right into targets. I would have expected something more lethal to distinguish itself from Thief? (I might be wrong here, but Krav always seemed more of a defensive martial art compared to CQC and Carp)
I feel like Hacker should retain the Binary Key - Being able to listen in to AI chatter would fit the 'opposing AI' theme
A bit worried about Professional losing their fallback weapon if they lose their sniper rifle/ run out of rounds, and unsure if the sniper rifle will be useful in a chase, but I don't have enough experience with sniper rifles to be sure here.
It might work to remove Microbomb and/or Storage and fill it in with some station-made implants? (Or maybe station-made implants, but hardened so that using your EMP implant wouldn't immediate murder you?)
Not sure if it would work well (Since you would need to supply autosurgeons, which means tots can really snowball with Robotics implant), but giving Bio Chip Bundle CNS Rebooter/SecHUD implant/Upgraded Cyber Heart (Or if the Bundle is too weak, Antidrop) that they can install themselves might work.