Regardless of CU or bank, keep an eye out for transaction-based fees. Some have a fixed number of transactions per month, and exceeding the limit will cost you on a per transaction basis. Some charge fees for certain types of transactions, incoming and outgoing. Number of checks, minimum balances, direct deposits etc etc.
If you don't expect a shitload of transactions hitting your account, you should be just fine. Or if you use an intermediary service like PayPal to handle the day-to-day, just watch for the monthly fee amount.
From a UI and functionality perspective, some banks' online business portals differ DRASTICALLY from the personal ones. And not in a good way. Seems like a lot of smaller local banks or CUs use a version of a third-party online banking platform (not bad, per se, just...clunky).
Even big bad BofA isn't too much of a hassle to deal with, anecdotally speaking. Sometimes when I would stop by a branch to deposit cash, I'd pop over to one of the "personal bankers" or enhanced tellers or whoever and just asked them about my accounts. S/he'd pull it up, I'd ask about the kids or the divorce or whatever, and "oh hey, by the way, can we get that monthly charge removed and those wonky overdraft fees that hit before our deposit?" *poof* fees gone. YMMV. :)