OK, I finally got around to giving this a try.
I couldn't make all the changes Phil suggested, but here are the changes I made:
-Fixed bug causing playback desyncs and differences between Blip's and Phil's Patched FCEU
(I think this should also fix the "FCEU sometimes changes a valid savestate to another savestate that resets the game" bug, but I've never seen that bug happen, so I'm not sure)
-Fixed bug preventing the auto-fire keys from working
-Integrated all
changes/fixes of FCEU version 0.98.13
-Integrated all mapper and board additions and fixes of the
fceu-mm project
-Incorporated a much better default palette
-Added Record from Start (power-on + wram clear) as default recording option (and previous versions can still play it)
-Added "Input Display" (activated by a hotkey, like the frame counter)
-Added "Toggle Read-Only" hotkey for switching movie playback/recording without reloading
-Made frame advance repeat after a delay if you hold it down
-Made frame advance pause the game if pressed while it's unpaused
-Made loading a save state show its graphics immediately even if paused
-Fixed bug that allowed key-up events to activate hotkeys when 2 hotkeys had different modifiers
-Stopped emulator from using 100% CPU power when left paused in the background for a while
-Added a warning to help catch if a save state becomes corrupted
-Prevented exiting movie play dialog while movie browse window is still open
-Worked around bug in DirectInput that prevented the Pause/Break key from working as a hotkey
-Changed the default key setup (it's still configurable and your old settings won't be erased)
Compatibility with version 0.98.12(blip) is maintained in almost all cases, which means that each version can play movies made in the other version (so you can watch previous movies with input display on, for example, and the process of verifying movies made with this should not change).