Biggest issue for getting away from the stock ROM is buggy behavior.
HK took a proven board designed *for* them, and hacked it up to switch to a bigger processor and a better sensor so they could stop paying royalties . . . and botched the job. The original designer came out and (surprisingly) without malice pointed out the hardware errors in the board and issues on the ROM . . . about the time people started seeing some of the bugs arise. HK's response was to put a note on their website to reflash to their 1.6 . . . which was also crap.
All water under the bridge. The stock ROMs on HK's KK2.1.x's are their cruddy port of 1.5. Buggy, doesn't read the gyros well so it doesn't tune consistently, really doesn't handle servos well (tri's), and occasionally decides to get confused and fall out of the sky. I won't say Steveis's latest is bug free, but it is a stable ROM and flies well. The PI gains in Steveis's are better than stock and generally flyable, but an untuned board flies like crap regardless of the board/ROM.
If you want to look at the laundry-list of changes they begin on pp.30 and go on for 5 pages (PDF):
http://www.rcgroups.com/forums/showatt.php?attachmentid=7345654&d=1417731690
On the positive side . . . The cloned kk2.1.x boards come stock with an old version of Steveis's ROM -- most common I've seen is 1.8 IIRC. That ROM is still missing some of the nicer updates, but is far more stable and functional than HK's 1.5. For once, the clones surpass the original