A few issues...

In no particular order:

My custom attribute colours never stay after closing and re-opening game - any way to stop this?
I use the Steklo skin, so I assume there is a file I could edit to do this?
- Not sure, perhaps ask on the Steklo thread & Tom can help

The Match Engine still seems a little off - I concede too many goals from tight angles, too many from opposing strikers running through without my defenders following, and a few little issues like that.
- Me too, I belive this is a known problem and SI will be releasing a big ME fix soon

Team talks - If I start as a Sunday League Footballer, my team talks have little to no reaction - I would assume that is because as a "unrecognised" manager, the players don't respect my opinion... I may be looking a little too much into it though.
- Me too. Sounds counter intuitive, but you will end up doing more damage, so stay silent for the first 8-10 games of the season, but give a Team Meeting if it allows you to. Once your team is doing ok, they will respect your point of view, at which point give Assertive & passionate talks like I have Faith, I expect a win, etc.

Whenever I close FM, Windows says an unexpected error has occurred - Anyone else get this?
I get this sometimes on my Mac, tends to happen when FM has been open a long time and my internet connection has dropped and the error is actually with Steam, not sure what to suggest, if it's not effecting your game, I don't spose it matters...make sure you save your game regually though (I've had FM crash a few times over the last week or so.)

There seem to be too many goals in both my games, and AI games... I very rarely see a 0-0 score!
- Agree there are loads of 6-1s and all sorts, I guess they want to reflect the crazy last two seasons in the Prem....? I'm not sure if they will fix this..even if they don't I don't mind, more fun

Team/player inconsistency - One game I will destroy a great team, the next I will draw or lose to a minnow - I know this can happen in real life, but ALL THE TIME!? - again, could be down to team talks, but I'm not convinced.
- Team talks do have an impact here, as well as tactics. I actually play more conservative against the lower teams, remember they will be playing in the same way as you did when taking on a bigger team...No pressure on their players, and they will be fired up.

There may be a few others, but these are the only things I can think of for now.