For the first question, it all depends on what you're looking for in a team I suppose. I can't tell you about the NL because I'm not as well versed with those teams (I play as the A's and mostly face AL foes). On the AL side, however, the two best teams are Cleveland and Texas. Kansas City is a close 3rd if I remember correctly. Texas is the more complete team, with a better farm system and higher salary cap.
If you're looking for rebuilding teams, I think New York would be an interesting choice. They're teetering on the line between contender and seller. They have young talent with premier prospects only a season or two out. Dweller teams like Tampa Bay, Minnesota, and even Oakland are for the die-hard players who are willing to scrape and claw to contend.
For the second question, as I've stated a few times before, I would recommend not using fantasy draft with this roster for two reasons: 1. I personally hate fantasy draft and it screws with the balance of the rosters. 2. I specifically designed and structured every team to resemble their real life counter parts. Equipment edits might not look as great when players are placed on different teams. But with all that said, once you download the roster, it is your's to use however you see fit.
I think you'll like the Phillies team. I know I do. They're a middle of the pack type team but could easily contend with some scheduling luck.
Now, for those of you who've downloaded the file, I would like some beta testers of sorts. I haven't had the time to go through a franchise and see how the lack of playing time affects their salaries as they hit arbitration and all those other rules. If some of you could do that for me and give a run down on any issues, that would be great. Thanks.