I'm playing an Erudite Necromancer. No regrets with my choice at all. Here's what I've found, as far as faction:
You won't start off KOS in Erudin. You'll be dubious to at least the guards and most merchants. Maybe you'll be KOS to the Paladins or Clerics, but I've never bothered to check, and I've never had a problem traveling through the city to the docks.
You won't be KOS to most of Qeynos, with the exception of the caster guild. There are a few wandering NPCs on this faction that make it dangerous to wander around South Qeynos without invis. Some people seem to have good luck in avoiding them, but my personal experience involved dying before I saw my aggressor. I stuck to the sewers since then.
You won't be KOS to most of Freeport. I'm KOS to the Warrior guild in the West (easily avoided), and various mobs in the tavern at the docks in the East (also easily avoided). I'm not sure if you start off KOS to the North Freeport guards, since by the time I got to the city I'd already killed enough bards to ruin that particular faction. However, it should be noted that even if you're KOS to the guards, you can still use the bank. Just run invis into the back of the bank, stand in the corner furthest from the guard, and you'll be fine. Don't attempt to use the merchant.
You'll be tolerated by some of the dark elves, although the Necromancer guild will be KOS. I can use the bank and merchants in Neriak after doing some faction work, but I haven't found an easy way to bring up faction with the Necromancer/SK guild.
Curiously, I was adored in Halas and Rivervale, although that hasn't stopped me from hunting both races extensively.
The biggest problem, in my opinion, with the Erudite Necromancer is that you're generally evil enough to be hated by at least some residents in the good cities, yet you're too human to be welcomed in the "evil" cities like Neriak, Grobb, and Oggok. I'm KOS to at least some factions in each of those cities. But faction isn't all that important to a Necromancer, and I can always find a vendor when I need to.
So, make whatever character you like! If you do end up as Erudite, make sure you get
this before you leave the island.