The TA, if you're unfamiliar, was created a couple of years ago by a voter mandate. Muni was in awful shape at that time (unimaginable, we know), and an voters needed an alternative agency that could actually get work done. And it worked -- the SFCTA has reduced congestion, fixed up 19th and Geary and Octavia, spruced up transit in neighborhoods like Little Saigon, and they're working on converting Caltrain from diesel to electric. In contrast, during that time Muni was busy being mean to a lady in a wheelchair.
If Muni took over the TA, it wouldn't make your bus run on time, or put up more NextMuni signs, or train bus drivers to be more friendly, or cut waste, or consolidate redundant lines like the parallel 31, 5, and 21. It would, however, mean that Gavin would have a bigger piggybank to dip into when he feels like strangling transit.
So, why does the TA work so well, and the MTA (that's Muni + some other street-related agencies) move so sluggishly? Well, our guess is that it's because the TA only takes on projects that it can afford; while the MTA is so ambitious, so underfunded, spread so thin, and so chronically strapped for cash and talent that it can barely stay in business. (The T-Third and Central Subway aren't going to help.) If Nat really wants to make Muni run well, he'll need to stop eying other agencies' money, and make the tough decision to cut costs -- and by cutting costs, we mean start eliminating services. That won't make him popular; but it'll make Muni work.