lots to talk about here...
first off, as for getting smooth shifts into 2nd, you can do it, it just takes practice as previously mentioned. this car is pretty fickle as far as shifts go, but once you get used to it, you can actually shift it smoother than any 5 speed ive driven (94 celica was my old daily driver, and my dad's 01ish subaru outback). my technique to get smooth shifts varies depending on how quickly im accelerating. if im taking off quickly, i find it shifts smoothly if you do give it some gas just as its about to engage. you dont need much tho, any heavy gas before its fully engaged will really work the clutch and make it slip prematurely. make the shift quick too, cuz again as mentioned before, that jerk will often come if you wait too long and the rpm drop back down to below the point you wanted to shift at. if im just farting around and shortshifting, my 1-2 shift is completely different. i'll only run it to about 3k rpm, even lower sometimes. as you're bringing your foot down on the clutch, keep on the gas until you hit the catch point and then let off the gas, as that will keep the car from lurching during the first part of the shift. then take your time shifting to second, let the up nice and slow through the catch point (not too slow, too much slipping on it is never good for the car, but just enough to keep the shift smooth). once i got used to the long travel of the clutch pedal, the ease at which it moves, and the release point, i havent really had any trouble shifting. once in a while when im not paying attention, i'll get the lurch and jerk, but just make sure to take notice when you make a good shift, figure out what you did right to make it happen, and try and replicate it every time.
second, i like the idea of starting out in 2nd when possible better than skipping 2 and going straight to 3rd from 1st. its a PITA to engage 1st from any sort of roll, so if you have any speed at all, drop it into second, accelerate slowly till it gets up into more of the powerband so you dont bog the motor too much (~2.2k seems ok to me) and then just continue on. much easier than having to deal with first from a roll. much like lestat, ive never been a fan of 1st gear in any car.
finally, no, skipping gears will not help your gas mileage unless it keeps you from wringing it out through each gear, which you shouldnt be doing anyway if youre that concerned about mileage. there are a ton of ways to boost mileage, but skipping gears isnt one of them. when shifted properly (by properly i obviously mean that applying to optimal mileage shifts, not performance shifts) through every gear, you should be able to shift up at about 2.8k which will drop you back to ~2k. of course acceleration should be slow and smooth, because goosing it to 3k wastes a lot more gas than taking it easier to 4k, so watch that too. there are a bunch of other ways to increase your gas mileage, but as far as shifting goes, thats the only way IMO. skipping wont help.
feel free to disagree, but to me it seems clear that revving the motor higher to make the 2 gear gap on the shift won't do anything but dump more fuel than using all the gears. i average about 25mpg (calculated, not from the on-board computer) around town here, which is mostly smaller roads, nothing over 55mph speed limit, moderate stop and go, but nowhere near as bad as city driving. i'd be willing to bet, though, that i could push over 30 mpg out of the MS3 daily driving, no interstate / highway miles. haven't tried doing a MPG tank, but i think 30 mpg is certainly an attainable goal for this car if driven right.
problem is, this car doesnt deserve to be treated like that. IMO there's no point in buying a performance car if you're gonna drive around with a stick up your ass trying to get 30 mpg. 25 mpg is still pretty good, and that's with me taking it up to 4-5k to throw my head back and giving the tire sidewalls some action through tight corners. to me the car just begs to be driven with vigor because it responds so fluidly to everything i do to it. i'll take the head snapping boost and shoulder throwing turns over trying to get an extra 5 mpg and driving like an old lady. go get a smart car for that.
/end novel. i apologize for the long windedness (stfu)