i have a heavily modded 250. the seat height is about 31 inches right now (stock is 29 inches). i am 4'10" with a 29 inch inseam. i can't touch at all. (giggle) for me, i don't need to touch the ground much at all to be comfy. one set of toes at the stoplight is about all i need!
but everyone is different.
the very most important thing to worry about when buying a bike is how comfortable are you on it, sitting, riding, moving it around in the garage, etc. don't worry about resale value, getting "tired" of the bike or anything. studies have shown that most people crash within the first year of owning a new bike because of lack of experience with the motor itself. now multiply that by being a new rider.
the ninja 500 is a sweet ride, but will have about a 31 inch seat height- there are some adjustments you can make from the rear spring, but i don't htink you'll get more than a half an inch out of it. the gs500 is a nice little motor- puts out less hp than the ninja 500 but not by that much (tho it does cost a bit more, i believe). but it's heavier, wider and taller than the ninja. i looked at the gs (the nekkid one) a few years back and it just seemed very cumbersome for a small person. i could have ridden it just fine, but pulling it out of the garage, etc. would have been kinda rough for me. like buying an older 600.
you may love the 250, you may hate it. it's hard to say.
i have nearly 16,000 miles on my 250 and am currently averaging 1 minute, 40 sec laps on the local road racing track with it, which isn't very fast, but it's about average for the class i'm in, which is filled with inline 600's and sv 650's. if you really want to get the most out of a 250, you will. it's all about how you ride it. take it to a track day or a race school and see what it's really made of.
if you're going to get a bike lowered, in my opinion, it's a waste to do it to any 500. it's going to cost a bunch and if you take the msf class and practice taking off from one foot, it will be easily resolved. have you looked at these?
http://www.hyosungmotors.com.au/gt250r.html
it's pretty inexpensive and recently i sat one one. seemed very narrow and light.