The Tavern

How much armor should I be trying for with a Naga or a Centaur?
Both have a low aptitude for it and get only half effect, while it still reduces EV by the same amount, which seems to me would make it pretty useless.

At what point would armor be better to take over evade?

Nagas and centaurs both have poor to terrible aptitudes in dodging and armor. This does not mean that you don't train and use those skills on them, it just requires more investment and slows down their growth in those areas. Those bad aptitudes and unfitting armor are basically necessary balance mechanisms, as centaurs (particularly) and nagas (after getting through early game and finding ways to compensate for slow movement) would be far too powerful without some drawbacks in these areas.

You should aim for about as much armor and EV as other characters. It just takes more to get there, centaurs in particular need to lean on their fast movement to pick their battles. With nagas you might dump a bit more into stealth early on as a defensive measure, you'll get ridiculously good returns there, and lean on poison spit like you life depends on it ('cause it does). Nonetheless you'll eventually want to get good EV and AC on all characters. (Or at least as good as you can get.)

The unfitting armor doesn't apply to the + level enchantment of armor, by the way, just the base amount. So you lose 3 AC from mottled dragon armor, for instance. Centaurs get an innate permanent bonus to AC starting out (+ 3, actually) and Nagas start with lower AC bonus, but it grows over time to be quite large. When you take these natural AC bonuses into account, Centaurs are only slightly worse off in most armors, Nagas nearly always come out AHEAD (ultimately) but even early on you'll break even in mottled. (By character level nine—which you'll reach almost certainly sooner than you'll get a mottled dragon armor.)

I keep mentioning mottled because it is an excellent armor choice for a lot of characters, by the way, and centaurs and nagas are no exception.

Just put different stuff on, check the EV and AC ratings, and put on whatever gives best total protection without making your spell failure terrible (basically, same thing you do with all species). The poor aptitudes are a drag, but just consider it part of the price you pay for a lot of awesome intrinsics.

Totally true- most of my Ce won the game with less than 5 ev - but you can still get good dodging value too, if you manage to increase their terrible dex (one example and second one).
Still, I'd wear a heavy armor and go around with 2 ev on a Ce 99% of time.