It's hard to say. Dan Briggs certainly had more personality; in the first season, especially the first half thereof, there was more exploration of the characters as themselves, more out-of-character interaction, even the occasional tension. The series' first two-parter, "Old Man Out," even had a scene with Dan trying to convince an old flame (or at least an old friend who wanted to kindle a flame with him) to join him on one more mission, just about the only time we ever saw the recruitment part of the process. By the time Jim Phelps came along, the individual personalities had been pretty much quashed.
On the other hand, Dan was a real hardass. He could be very cold and ruthless and went to pretty dark places sometimes -- in one episode, appropriately titled "Shock," he even murdered an unconscious man in cold blood after having subjected him to electroshock therapy and torture. So Dan was kind of a scary guy. While Jim's team did their share of "set the bad guy up to be killed by his own allies" kind of schemes, Jim never seemed as ruthless as Dan. Graves made him a more avuncular, approachable figure. So even though Jim was a less well-drawn character, I guess I'd have to give him the edge as a favorite.
That said I really think it would have been better if Phelps had been the only regular. The other members of the team would be drawn from a rotating group of maybe a dozen agents, with Phelps choosing the best mix each week based on the mission's needs.
They stated with something like that, Phelps going through dossiers and choosing the team, but it was dropped by the third season. And in any case he always picked the same agents. I don't think there was ever a single guest star agent. It was a bit disappointing.
Well, actually the dossier scenes were pretty much a token gesture in the second season. In the first season, there was a fair effort to vary the team composition; only 15 out of 28 episodes feature the whole team, and quite a few episodes had guest agents. This was particularly so in the earliest episodes, where the guest agents tended to be the dramatic focus of the episode -- Martin Landau (who was originally intended as a guest star) and Wally Cox in the pilot, Albert Paulsen in episode 2, Mary Ann Mobley in episodes 4-5, etc. After that, the stories tended to focus more on the regulars (if you count season-long "special guest star" Landau as a regular) with the guest agents being more in the background if they were there at all, though there were a couple of exceptions (indeed, "Elena" revolved around Rollin on a solo mission, so technically none of the regulars participated except Dan in the opening scenes).
But in the second season, things became much more standardized. Every episode featured at least four of the five regulars, and 80 percent of the episodes featured the entire regular team. Only about ten episodes featured guest agents in small roles (eleven if you count the one where the "guest agent" was a trained cat), plus a couple where they had some outside assistance by non-teammates. So usually the opening dossier scenes where Jim picked his team were superfluous, since it was usually the same team with only minor variations. They dropped the dossier sequence in the second-season finale.
From my blog, here are my overviews of the first two seasons, with breakdowns and statistics of things, and with spoilers:
http://christopherlbennett.wordpress.com/2010/03/05/mission-impossible-season-1-overview/
http://christopherlbennett.wordpress.com/2010/06/17/mission-impossible-season-2-overview/
I think something like the original "variable team" intention would work well in a modern TV remake, since it's common for shows these days to have large casts that don't all appear in the same episodes.
