Well brother. It is a tough decision I know. Every one has his own preferences. Some people look at luxury, some at saving money. The best is the way to look for the best possible luxury affordable with your pocket.
Sir, the gas kits are best suited for manual rides. If you want to install gas it is better to go for some manual transmission ride. (Although people say that there are special kits for CVT but I have no experience of those)
Secondly, the mileage calculations of gas driven cars are always better than petrol cars. The two important factors in these are the "way you drive" and the "amount you drive". My vitz 1.3 has given me max 15.8 till now because I never accelerate quickly. I always turn off engine on longer traffic signals and stop points. Further, I bought vitz because my average drive per day is only 12 Kms. If a car on gas cylinder gives 150 Kms and that cylinder gets filled in 720 Rs. then this ride is giving us almost 4.8 Rs per every kilometer. If a car is on petrol and gives us 15 Km/L then it is giving us almost 6.7 Rs per every kilometer. This is not a big gap. But this gap will be widened if we drive more and more kilometers per day. For example the person who drives 10 Km daily, will spend 48 Rs and the one on petrol will give 67 Rs. It does not feel big difference still. But think if some one drives 30 Kms daily on average. He will have to spend 201 Rs. on petrol car which is very expensive when campared to 144 Rs. on gas. The more you drive the more will be the gap. So, you must consider both factors, "way you drive" and the "amount you drive" [Remember! I have been very polite in giving the mileages. It is very tough to get 15 Km/L from most of the petrol cars, and, most of the gas cars give far more kms on one cylinder (more then 150 Km as I have estimated) and many people drive more then 40 Kms daily. If you do 1500 Kms every year that will mean almost 41 Kms daily average.]
There is another problem for JDM engines. They are used with better octane number fuels in japan. So, you will have to mix high octane in it after few refills otherwise the you engine will knock. This will also increase burden on you pocket. [Due to this fact I bought 1.3 instead of 1.0 which has less tendency to knock due to low octane fuel]
And yes the parts are expensive too. Even the labor is expensive too. But yes, tyrone_40 bhai is right, if you will go for OEM they will last long. But while buying you will feel the dent on your budget.
Vitz resale depends on the place you are living\selling it. At the moment vitz is the best selling ride in imported cars in metropolitan cities. So, resale should not be a problem. But this is true that it is not as good as local cars.
Well yes the street mechanics are not very well trained at vitz. But there are good shops present which have all the skills required to maintain vitz.
Sir, Overall vitz is a very good car. You will surely enjoy every single second passed driving it (except the fact that it crashes on most of the speed breakers). Now, the decision (though very touch) is all yours
Best of luck,