Glad you're turning this reminder off for perks. I often play with some points unspent and it was pestering me on every battle. Don't see much of reason for anybody not wanting to rise skills/stats though, so that's prob. all right. However, if there will be any in the future, some people might ask for an option to turn it off. Just making a note. Majority will be glad for this feature, of course.
As for recruiting allies later being harder. In the past, it was often 10+ lvl difference and I tell ya wasn't forgetting to lvl up right on their first turn, provided they managed survive up then... Yeah, what perceived definitely harder was right at the start: can be handicaped at re-position but also the higher the lvl difference the higher probability an ally acts last in the first round (np for Elena though). In the past got Emilia destroyed like this before she got the chance. However, their missions got easier post EA.
If you will ever revisit this, think would be neat to have a chance to lvlup before the battle. Perhaps like Sam at the start? Initial conversation can end with the 'character sheet' button instead of the launch arrow one -> that would allow us to familiarize with a new ally, check their inventory and distribute any points beforehand. And then from there - the arrow button launches the battle.
Additionally, what about stats. If an ally is recruited early you can distribute points how you want in the future, whereas if many levels later the ally has stats already assigned and you can't change anything. This autoleveling thingy is a bit stubborn in assigning points anywhere else than to Fleetness. Will you deliberate stat points?
Edit: Oh, forgot there there is also the equipment. Don't they have the same starting one? With Emilia, Sam starts not so near so not easy to pass her an armour or a better gun. Would be neat if he can throw it. Think I've used smoke grenades to shield her.