Interesting and well formed thoughts about Siege.
I really like your suggestions 1 and 2 (except that 2 can't really happen without new maps). Mechs going faster based on how much EU they carry is brilliant - as long as that boost in speed is only in effect until the teams ship launches and the AA goes live. I wouldn't want hoarding EU to give a speed boost to become a new meta in Siege for improving defense of the AA - but I'm open to being convinced otherwise.
I do not, however, agree with you on some of your other points:
I don't think that collecting EU discourages combat. I actually enjoy how it requires strategic decisions about knowing when to start collecting, when to wait and spring a trap, when to ambush and, of course, when to run. And I think the running and chasing is actually a great deal of fun - for both players involved, as the feeling of either "getting away in the nick of time" or "shooting them down just before they make it to the base and stealing back their EU" is pretty invigorating.
Also, I actually like the dynamic of combat for control of a static point. I don't think it's more 'limited' than the style of combat in TDM, I just think it's different and requires just as much thought... and maybe a bit more courage (if you're doing it right). You've got to be strategic about how you get in to the fray - will you charge in hot, come around from behind, the side, underneath? Will you wait for your team and go in with a united front, or is it better to go in now and create a distraction and some chaos while the others work their way in behind you? And I don't see where it detracts from mobility. Yes, a heavy mech may be better at "holding", but it takes them much longer to get to the AA and they are much more susceptible to getting flanked and CC'd by lighter, faster mechs. A good team needs a good variety of mechs to be effective at Siege.
I also kinda like the in-game debate over when it is time to focus on trying to retake the AA or time to fall back and shoot the ship. And there are so many little factors that can play into that decision... factors which reward a team who chooses to (or just naturally) work together and punish a team which does not work together. Siege is a "teamwork" game type - and the outcome is dependent on it. I like that.
And I actually like the mechanic of shooting the ship. That said, it could be more challenging. It might help if those ships were a bit higher up so that players had to choose wisely which weapons they bring out for the job and have to lead their shots. And I would be in favor of having the base defense turrets range reduced in correlation to the enemy ship proximity to allow the offensive team to get in closer to deal with campers shooting the ship. That's probably the most broken part of shooting the ship - the safety that the base defense turrets give them. Falling back to shoot the ship is a good tactical move when done at the right time, and without that mechanic, Siege matches would become lopsided and be finished far too soon in too many cases - but significantlyreducing the range of the defenses in correlation to ships distance from the base... until it's almost non-existent when the ship is right over the base would certainly create a bigger sense of excitement and risk to the tactic.