I have GMd it multiple times although mostly just one- or two-shots. I really adore the Mouse Guard setting, but I found the rigorous structure quite limiting as it almost discourages following up on organically occuring story moments.

Luckily, the basic system is really quite general and will survive a lot of fiddling around with it. So what I do is simply not using the systems that I don’t like, and emphasize the parts I do like. I try to preserve the general feel rather than the exact mechanics:

Yes, you’re strictly on a mission, but that doesn’t mean you are forbidden from searching alternative solutions, even if it deviates from the initial plan.

I like the element of having some downtime inbetween the action, where “everybody gets to do something” but without the strict check economy. (Also having to spend checks to try and recover from conditions while your friends are having fun in town is just not great in the first place.)

I don’t use the checks at all because I simply don’t get the appeal of such meta negotiation systems. The players can simply use their traits in favor, and the GM is allowed to use them against them when appropriate - the Fate and Persona points offer more then enough options to let the players emphasize when a roll is important to them.

I don’t like that the “twist” resolution method encourages the GM to set high obstacles so that something interesting can actually happen. Sometimes it is fun to come up with a twist on the spot, but often times just sticking with a more traditional pass/fail style tests is the better choice. Though I think the system lends itself bery well to thinking about how different degrees of success and failure could look like.

However, there are some elements of the system that in my opinion need special attention when deviating from the “intended” style: One is that repeated rolls on the same skill have implications for how fast the progression is when compared to skills that come up less often. I usually try to avoid too many repeated rolls on the same skill, but if that is not possible in the situation, consider using a similar system as in conflicts where only one success or failure can be earned per skill per “scene”.

Another thing to consider is that giving out multiple conditions on multiple players has a really strong impact on the conflict mechanic - it really makes the group much weaker. With a more flexible number of rolls, it is quite easy to accidentally weakening the party too much.

Side note on the conflict mechanic: it doesn’t feel great in larger patrols, even if you split it up into multiple conflicts, and I would understand not liking the rock paper scissory feel of it in the first place. Luckily, the system lends itself rather well to alternative resolution methods like one player or the whole group need to gather X successes in Y rounds (I like to style these after the “dramatic tasks” of Savage Worlds).