I agree with practically every core issue you've stated here, but I do have issues with some of your suggested solutions. Particularly, I'm a big fan of flavor for a game of this nature. While things like "transfer windows" and "salary caps" would make the game far more fair, balanced, and predictable, it completely ruins the immersion of a medieval fantasy setting. So while I do think there's certainly more to be done about how transfers and contracts are handled, I want a system that would fit in-universe.
To illustrate a bit more about lore-friendly solutions, let's take your point about tavern generation, for example. It's definitely good to generate units that are tailored to the level of your guild, but while it definitely doesn't make sense to be able to build a roster of 80+ in the backwater bracket, it equally doesn't make sense to never be able to sign even one - much less be able to see one at all. So let's think about this from a medieval fantasy setting. What kinds of individuals might we see visiting a guild? Well, hopeful commoners trying to get appraised for the first time as they're entering the adventuring world for one. Maybe a hero returning to his hometown after a long journey and deciding to settle down. Maybe some mercenary types who have been driven out of their home land and need a change of scenery. Even a small guild may see all kinds of levels of adventurers. BUT, whether or not that guild would be able to SIGN that adventurer to their guild is an entirely different story.
This is where renown can come in as well. To illustrate further, here's a fictional scenario: after a long and storied career, a legendary adventurer decides to hang up his boots and start his own guild in his hometown. Despite starting from nothing, his fame precedes him and some higher quality adventurers decide to sign up for the small guild - placing their hopes on what the guild would become rather than what it is right now. For a Football Manager equivalent, this could be like Wrexham AFC after its takeover by Ryan Reynolds and Rob McElhenney. They signed EFL1 caliber players despite being in the National League just on the promise of what the project would become.
Again, I agree with practically all of your points as far as the issues that you're pointing out are concerned, but the solutions can be a bit more creative I think.