While I will readily admit that much of my like of Magus comes from his character design, I think you are being a little harsh.
The advantage of the high magic stat is that the Fire/Ice/Lightning/Dark Mist attacks do a ton more damage than any other characters, as well as allowing him to exploit multiple enemy weaknesses to boot. This allows you nuke random encounters in a far more proficient manner. If I recall he also has the most/very high TP, though I could be mistaken. (Seeing as most of the post game my characters have 99 I don't think its really relevant)
Also, he has his own 'ultimate' equipment which is extremely easy and fast to acquire. You can easily run into the fort, grab it, and leave right after you get the Epoch back. Then do the other side quests in whatever order you fancy.
I don't think it really matters if he thought he could solo Lavos or not, it was more a consumed with revenge he was going to give Lavos everything he had or die trying. More of a personal score to settle, not a logical battle plan in the least. (I have soloed Lavos before with Magus, so it is possible.)
As for the ugly, I really liked his character sprite, however I did find his character portrait and FMV appearances to be somewhat lacking. As for the apathetic/quiet/loner archetype, in most RPGs I usually consider the bulk of the party to be idiots that I wouldn't want to talk to. If a character has the same attitude I can't say it doesn't enamor them some to me.