Before anything else, I'd like to state that this is easily my favorite mod for warband as of now. The setting, the refreshingly different pace of gameplay and the music make for an altogether exceptional experience. Here are some things that I've noticed:
The gates are bugged in my freshly updated 3.0 -> 3.1 game, precisely same as the previous posters. I'm not sure what more to add, as everything I could state has been said before.
I feel the new worldmap graphical update is too bright, I find it hard to see the tiny grey bandit parties and even some of the clan armies at times. At first I was pleased to see a bit less grim worldmap, but frankly I think the new one needs a drastic tone-down in the contrast department.
I'm not sure if this is intentional, as it has been quite some time since I last played any warband for quite some time, but I believe bandit lairs respawn nearly with no downtime. I can't recall if this behavior is the same as vanilla. I found them quite lucrative to grind out with my companions after I memorized the spawns.
Again, I am not sure if I'm correct, but I believe the capturable neutral outposts count towards your tax inefficiency, even if they don't grant you any direct taxes whatsoever. On the same topic, I feel the outpost troops are quite weak, and I don't see any point to use any of them unless I had to frantically reinforce a town's garrison vs an impeding siege. The fact that most outposts are a bit out of the way doesn't help.
When talking to the administrator, he always states that our spies haven't had the time to report back regarding the lord's mood, even if the fief is awarded the very next day.
I'm practically certain that looting is bugged when it comes to fighting many troops that have the same gear. I typically have superior loot when fighting 40 woku pirates, compared to 40 hatamoto deserters - which at the very best drop a single "set".
The new matchlock animations roughly doubled the time it takes to reload, is this final? After that change I'd likely replace all my hatamoto gunners with archers, given the opportunity.
The Ezo warrior parties typically do nothing but lounge around Hokkaido, and there are some 20-30 parties of them in my game that will never fight any caravans or merchants. Perhaps the potential spawns should be closer to Hirosaki, or Katsuyama so that they're not entirely pointless unless the player goes out to fight them?
I think a few more troop types, or at least unique troops would help with some much needed variety. I understand that it is historically accurate, but the fact that all clans share 80% of their troops with one another makes each of them a little more bland. Perhaps just a unique bodyguard troop type available by Great Lords, or an unique troop you can edit the gear of when you found your own clan. From a gameplay perspective, the Ikko-Ikki are the most interesting faction purely due to their troops.
I find that the available mercenaries of the "Hired Guard" tree are much too weak.
Some Western/Christian involvement would be interesting, beyond Wirriam-sama's and Francisco's RTR missions.
Oh, and the enemy battle AI is often quite weird, but frankly I haven't played a warband mod where it wasn't.
This should just about sum up everything I can think of at the moment.