Even Perez Hilton sometimes compares these shows. I like both, but prefer HIMYM. There are many simple reasons why they are different, so here are just a few:
1) 5 vs 6: This may seem extremely minor, but it is a very different dynamic. The plot lines of friends episodes often (but not always) follow 3 pairs of the friends doing various things together. On HIMYM there seems to be mais intermingling of plots (in my opinion).
2) Inspiration: HIMYM is loosely based on Carter and Craig's lives. They are the creators of the show and the idea started somewhat autobiographically.