Bowser is probably Ness' best matchup. Slow, huge target to hit with PKF, even if his crouch prevents hit stun, just keep throwing from a distance. Yo-yo off the stage = death.
Anyone who says Falcon is in our boy's favor, is either misguided, or hasn't played a good Falcon. I believe Ness has four kryptonite match ups, if you will. Those that without sheer excellent play, give Ness an extremely hard time. They are:
Samus, Mewtwo, Falcon, and Link. Samus simply cannot be comboed, combos Ness hard, has amazing stage control, can easily SDI PKF, and lives forever. A good Samus will utilize the non linear side of recovery to weave through PK Flash off stage and safely return to ledge. Mewtwo has so many tools, cannot be comboed easily, also SDI PKF easily (floaties man), teleport past PKF to punish, kills off the top super early and can punish Ness' recovery. I played with Emukiller and Frozen this weekend, Frozen, being around the same skill level as me, and they both handles Ness so well. Emu even saying that there isn't much Ness can do that doesn't get punished. Falcon has super free combos into knee. Down throw > knee is guaranteed regardless of DI. He's super fast and weaves around PKF no problem. Easy to punish off stage, but his stage control is just so good. Link has auto combos with his boomerang which will hit you eventually. All he needs to do it camp with projectiles. Crouch into WD back boomerang trumps PKF approach. Played with Aklo this weekend, friendlies went back and forth because he didn't know the MU so well, but when he got hits, he confirmed into early kills pretty easily. BTW, Aklo is a 13 year old kid that beat Emukiller in tournament 2-0, LOL.
Anyway, those are my thoughts.