Thoughtful initial post - welcome to the Org Rhubarbmisterwellington. But once you've played the game a fair amount you may start to look for ways to make the game more challenging to give it legs and that would imply NOT doing a lot of what you suggest. For example, never retraining units makes campaigns quite interesting - as you can't magically resurrect your veterans.

In BI (at least, as Romans),I find sieges and rivers seem to become important than in RTW vanilla. But the AI often does not seem to be able to cope with them despite a massive numerical edge with a horde. I'm not sure what houserules would be best to try to offset these AI flaws, as to totally forgo river defences and autoresolve sieges sounds a little extreme.