I was in the same situation a few months ago. I decided to go with Neo CD, and I'm still happy with my decision as it is the most cost and space efficent way to collect and play Neo games. However, I wouldn't recommend the Neo CD to you over MVS, becuase it does depend on what games you want to play.
If you want a Neo to play games like King of Fighters or Last Blade, forget Neo CD, The load times do get out of hand on those fighters. Also no fighters past KoF 99 are available on Neo CD. However, other fighting games like World Heroes and Fatal Fury load pretty quickly.
If you want a Neo to play Metal Slug games, forget a Neo CD. Only Metal Slug 1 and Metal Slug 2 are available on Neo CD. And while these both play great on Neo CD in my opinion, you're still missing out on Metal Slug X and Metal Slug 3.
Shooters are all great on Neo CD. I haven't played a shooter on Neo CD that had too long loading times (including Pulstar). The only problem here is that Blazing Star is NOT on Neo CD.
All the older games work great, and I highly recomend Neo CD for games like Puzzle Bobble, 2020 Super Baseball, and League Bowling. All these games are excellent and they only load once for about 20 seconds right in the begining and then never load again. Plus, prices on these games only range from 10-30 bucks.
So if you're not really too concerned with the newer games that won't appear on the system, or with the KoF or LB, I say go for Neo CD. Like I said, the price is right and it saves space. Sure, MVS games can be pretty cheap for the older games too, but depending on how you want to play the MVS games, it will be more expensive than getting a Neo CD system and will take up a lot more space if you go with a Cabinet.
However, if you have $500 to spend and want the best arcade experience, go MVS and get yourself a nice Neo Candy cab.
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