My favorite support set is Croagunk and Sylveon.
Since Croagunk gives a defense debuff to the opponent even if they block it, it is extremely useful against both close range fighters since it slows down the match by dissuading them from approaching and zoning characters since it can be used to control their movements and even lock them in the corner. Sylveon on the other hand recovers a small amount of health and buffs my defense. That may not seem very impressive, but that defense buff can often be the difference between surviving an opponent's burst attack and getting KOed by it. I've also used it when I've gotten a large life lead on my opponent just to make it more difficult to make a comeback.
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Pippin (Peregrin Took)
I don't think that is the reason why Pachirisu and Magikarp have such long timers. The way that they were designed makes me believe that they were intended not as a way to get in on zoners or break combos so you don't get punished as hard for mistakes. Instead, I feel that they were intended to make the mid to late portion of each round easier.
If your opponent has a life lead and starts playing more defensively in order to force you to approach, then Pachirisu can be useful since it temporarily takes projectiles out of the equation, which can be useful if your character has better normals that the opponent. Magikarp on the other hand can be useful if you have a life lead on your opponent. It takes about 50 seconds for Magikarp to charge, and by then the chance for a time out to occur is high. If your opponent is behind on life, then Magikarp's ability to break combos can make it legitimately difficult for you opponent to cause any real damage to you if you are playing for a time out.
That is just my two cents on why I think the characters may have such long charfe times. If anybody disagrees or has a different opinion, feel free to add in.