Updated! Welcome to the Club

and you're really lucky that you already have car at your age of 17. Be thankful for it alright

Myvi Standard -> It's the most basic version which does not have ABS. No Spoiler. Only Rim Caps given. Don't really recommend this unless you are really in budget of getting a car around that price
Myvi Premium -> Has all the basic functions (ABS, EBD and others), If you are asking between the 3 variants of 1.3 Myvis. THis is considered the most value for money.
Myvi Elegance -> Basically, It's ALMOST the same with the Premium version which it has all the functions just that it added Bodykit, Spoiler, Multimedia Touch Screen Player and Leather Seat. IMO, It's not worth the money at all as its RM7000 more than the Premium and its even more expensive than the SE variant.
Myvi SE 1.5 -> 1.5 Engine which gives you more power, Semi-Bucket Seat, Multimedia Touch Screen Player for Auto Variant, Better looking bumpers and outlook (More Sporty looking), Dark Colour interior. Considered the most value for money if you are considering for a 1.5 engine.
Myvi Extreme 1.5 -> Basically its like the Myvi Elegance, not worth the money as its just some cosmetic changes like adding bodykits, bigger spoiler, leather seat. IMO, Extreme look is kinda overdone for me...It really looks too extreme. No offense to those Extreme owner though.
1. 100% town driving -> Basically, of course a smaller capacity engine would have better Fuel Consumption but looking at our members that own a 1.5 and 1.3. The FC doesn't differ much
2. 20% long distance, 80% town driving-this situation where you stay in town all the time and balik kampung once/twice a year? -> Basically, of course a smaller capacity engine would have better Fuel Consumption but looking at our members that own a 1.5 and 1.3. The FC doesn't differ much
3. 50% long distance, 50% town driving-balik kampung few times a year -> If you are travelling longer distance. I would say a 1.5 engine is better as it has more power
4. Value for money. Which minimum spec you should go for -> For 1.3 (Premium Spec), For 1.5 (SE Variant)
5. How good is the manual transmission or should I just get the auto and be done with -> If you are driving more on the city better just go for Auto as you will be stuck in the jam most of the time
6. Is there a difference in the ride quality and NVH among the 4 different versions -> Not much difference in terms of ride quality but P2 claims that they have made the suspension for 1.5 more stiffer due to a more powerful engine. NVH is all the same
IN CONCLUSION, Basically if you are considering a Myvi, You could narrow down your choices to the Premium Spec 1.3 or the SE Spec 1.5 as both of them are considered the most value for money between all other variants. If it was me, I would go ahead for the SE 1.5 as FC really doesn't differ much from the 1.3. Moreover the outlook looks better with Semi Bucket Seat and also the Multimedia TouchScreen Player with GPS. It also gives you more power in terms of Pick Up.
However, bare in mind that Myvi was always a city car as its small in size , good FC and easy parking especially in the city. It was never mean to go high speed and do some hard cornering unless you are planning to mod your ride making it much more stable. Since you already mentioned you need a bigger boot space and travelling like 700KM long distance, I would say Saga is a better choice for you although I own a Myvi. It gives you better stability and also a boot space to put all your laugage inside. Both cars has their own Pros and Cons. If you are asking about the outlook and interior, I would say Myvi has better outlook and also interior.
I guess thats all for now. Hope my REPLY did helped you in making your decision.
Updated! Welcome to the Club

You can become part time Myvi salesman already bro.