I'm pretty far in at this point (chapter 20ish on hard) and I've decided I don't like the pair up mechanic at all. It seems to easily remove all thought I put into positioning my units because I can pair everyone up so that no weaker characters are on the field during the enemy's turn. I don't even pay attention to attack ranges anymore. And the stat bonus for taking the approach of pairing up means there is only benefits. Hell, with S rank pair ups both units usually end up attacking anyway.
Rescuing people in fire emblem 9/10 was a much more interesting choice because while a unit in danger could be protected there were a lot of drawbacks to it.
If pair up is going to provide stat boosts and extra attacks, then I think you have to take away the complete protection of the 2nd unit. Give the enemy the potential to attack the unit in back or add some other kind of threat to it.
As it is now, I just stuff my healers/mages into the back pockets of my tanks and march forward.
The pair up mechanic is a game changer, there's no doubt about it. I do think the guaranteed and constant ability to protect weaker units can be a small downside to the mechanic, as you've mentioned, but I think the upside is worth it. It's true that healers and mages stay protected when they are tagging along as a support unit but they don't gain EXP at a reasonable rate in that role, so if you want them to be useful you'll still have to expose them to danger at some point. On top of that, if you want to use a healer you'll be forced to make them the lead unit which could leave them open to attack (requiring you to think about your positioning).
The upsides of the pair up mechanic are very enjoyable and impactful to the overall FE formula, I think. I like that relationships now have a huge impact on the way that a battle plays out, and also that units who have a bond formed between them can help and protect each other. The stat bonuses provided from pairing up are also a great addition and can require some additional strategy to manage (if you want to match up units that will benefit each other in very meaningful ways).
Overall I think the pair up mechanic is a lot of fun and an interesting new wrinkle to the series' mechanics. It is extremely powerful, perhaps a little too powerful, but there are enough trade-offs to keep it from feeling broken to me (bad EXP gains for the support unit, less actions per turn, lessened ability to control areas of the map, etc.).