I don't want to say that we're better than the Ri quoted in tosfot, but is there a reason that some brachot start off with the 'l' prefix (L'Haniach tfilin, L'hitatef batzitzit, leishev basukah, etc.) and others start with the 'Al' prefix (Al mitzvat teffilin, Al Biur Chametz, etc.)?

I didn't have too much time this morning, but I was looking at the Rosh, and he had this whole thing about the immediacy of the mitzva following the bracha. Basically, he quotes the Rabbeinu Tam who says that anytime something starts with 'Al' it means the mitzva will immediately follow (above examples, plus Al Mikra Megilla, Al Hatevila, Al Netilat Yadayim, etc.). If the prefix starts with the 'L' it means there might be some delay until the mitzva starts.

I like this answer, but I was wondering: how come the tosfot didn't quote the rabbeinu tam, if he quotes him all the time?

Also, are there any other answers/explanations out there? My maggid shiur seemed to say that this was a big machloket, but didn't get into it for lack of time.

The Abudraham has a discussion of this issue. He starts off with R. Tam's position (al = immediate, le = not necessarily immediate), continues with a different opinion by the Rambam (al = for others, le = for oneself) and then the Ravad's critisism (al mikra megillah), and concludes with yet another reason (al = can be done by a shaliach, le = can't). The basic problem is that no rule works for every case (a corollary of what I said in another thread that halachic rules apply only when they apply). Significantly, the Abudraham was a contemprorary of the Ba'al Ha-turim, the Rosh's son and by and large follows the psakim of the Rosh and further clarifies the positions of the Rosh.

If you want me to scan the Abudraham, let me know.

In any event, I don't think R"i is contradicting R"T (which would be unusual for R"i who was the nephew and student of R"T). I think he's just stating the obvious that in spite of R"T's general rule regarding immediacy, that rule doesn't work in all cases.

There is a long arichus in the Ran too here.
(Daf 3:2 midafei Horif)

And I suppose the Ra"n is a big gadol?