I imagine it would be difficult managing social links if that were to happen. Personally while I found it awkward as well, I really didn't mind it as much as I was too in love with the game to gripe over one minor problem.
I just finished it today... Nyx was surprisingly easy, but that's probably because I went on a mad grind to try and get Messiah earlier on.
I'd have to say my favorite Persona was Metatron. He wasn't particularly powerful, but he had a lot of Repel Element skills on him, and Magarudyne and Megidola, so I used him more than my Thanatos (w/ Tempest Slash, Survive Light, Megido and Die for Me!) up until I made Messiah (Megidolaon, Salvation, Repel Dark, Die for Me!), and Satan (Maragidyne, Die for Me!, Megidola, Black Viper, Repel Light).
I maxed Lovers, Chariot, Tower, Sun, Hierophant, Death, Fool, Judgement, Magician, Hanged, and Hermit. Temperance and Justice were reversed because of my negligence and Empress was also reversed because I went out with Priestess (Both were level 7). I'll do the second cycle later to get everything maxed. Now onto Soul Nomad and Wild Arms 5 for me.