The Aircraft Autopilot doesn't need any more bug reports, see:

#1549
#1494
#1472
#1422
#1420
#1344
#1336
#1335
#1334
#1330
#913
#625
#463

It needs PRs to fix those issues, or else the module should probably be deleted. Nobody is working those bugs and there is literally years of work left to be done in areas dealing with rockets in MechJeb.

The Atmosphere Autopilot mod is recommended.

NOTE that it'll be necessary to press the P hotkey to disable Atmosphere Autopilot and use MJ (for rockets)

(FAR stability assists should also be turned off for the rest of MJ to work correctly)