It honestly depends on what you want the car for. If its a DD and you need room then the MS3 is better. If it's a DD and you don't need space then the S2000 is better. I drove an S2000 for 5 years and traded it in on the MS3. I simply got sick of all the road noise. Sure a Vert is fun, right up till the top starts to get loose and the wind noise drives you nuts. You then find out that it will cost about 2k to get a new top or 3k to get a hardtop
Now, if you want to Mod then the MS3 is better unless you have a ton of cash to toss at it. $500 in a MS3 will equal death to any bolt-on S2000 on the highway (They will get you from a stop but you will catch them eventually). A Simple MBC/Map Clamp puts any S2000 in the dust other than a FI'd one.
To get the power from an S2000 you're looking at a Turbo/SC. That's a Cost of 3-5k depending on the kit. Sure that alone should be enough as the S2000 gets 100WHP just from an SC bolt-on.
However, if you're like me you will not stop there and want to replace everything power wise. Most TBE's (if you go turbo) will cost you in excess of 2k. Stroker kit is another 2k or so. ECU Upgrade is another 1k give or take.
The end of the day you will need to invest 10k or so in an S2000 to give it serious power.
If you put 10k in the MS3 the MS3 would probably still beat the S2000. Unless of course you do a Supra Engine swap in the S2000
Again it depends on what you want the car for. The only mod I ever put on my S2000 was a CAI. Everything else I could not justify due to the extremely high cost for such little gain. A fully bolted on S2000 will net you about 10-20WHP if you're lucky and put you out close to 2-3k depending on what you purchase.
My last Dyno day was with the S2000 guys. The best S2000 pull was like 220WHP with Race gas. I put down 250 and was heat soaked like crazy. Most of the S2000's that day could not break 200WHP and where between 180 and 190WHP.
So unless you suck at driving or your car has an issue, stock to modded (equal money invested modded), the MS3 should win every time.