This video might help seeing the mechanic from a different perspective (as a future game designer, I also have been thinking on many mechanics of games, and this is quite an issue, balancing them; sorry, forgot how to add a video from youtube in here lol been ages since I posted on the forums) http://www.youtube.com/watch?v=EitZRLt2G3w&list=PLhyKYa0YJ_5BkTruCmaBBZ8z6cP9KzPiX&index=32
Anyways, it is clear the mechanic was introduced to allow players new to the series to have a chance to adapt to what Fire Emblem offers itself: support system, offering occasional guards to avoid damage when you didn't see some movements coming, and extra power to defeat enemies that could be a problem to handle or could pose a challenge you were not really sure if you could handle when you're barely beginning (pretty much like the casual game mode was meant for newcomers to the series when introduced); including it again could be for many reasons, but I want to think it stays the same, attract new fans to Fire Emblem.
Sure, it needs balancing, but the thing is, that we're given the choice to use it or not when the option of pairing up is given; at first, it is very tempting to rely a lot on the Pair Up mechanic, it makes the first missions a bit easier, but as it is mentioned in the video, the game itself never says or suggests players 'Hey, there are other ways you can work around this map besides Pairing Up' because all we had to do was Route or Defeat the Commander, easiest way to do it? Pair Up, there was no need to actually try another road. I'm also supposing the mechanic was made to speed up the game a bit, since nowadays most games nowadays are multi, or have things to unlock. Still, it's just my opinion on this xD
Pair Up was nice, I admit I overused it and it also made the game very lineal in a fashion to a point I got bored of playing the maps, like most say in here, it could be fixed to be more versatile, but then again it would need more hours programming or re-designing it, and the choice will be made by IS, so let's see how it fares in the future.