I'll weigh in on this - I have test driven a couple of MS3s over the years, and owned an '01 Viggen for the last two years (sold recently - still pining!) Reason for sale was that with 3 cars, one had to go - it wasn't going to be the track miata, and the recently bought '00 Silverado that tows it occasionally has just proved too useful. So, bye Viggen. I sold it to a neighbor. He's very happy!
If you don't want to deviate from stock then the MS3 wins acceleration and handling easily. Adding go fast parts to the Viggen will probably get it up to stock MS3 capabilities, and for a lot less total $$s. Where the Viggen really shines (even stock) is as a deceptively quick, good looking, comfortable, (and utilitarian) executive car. People routinely thought it was worth twice what I paid, or more. And you do NOT see them coming & going - mine was a 5-door hatch and in two years in OKC I never saw another 5-door Viggen. I believe it was actually conceived as an M3 competitor, and would hold its own as far as acceleration with the E46 M3s but not the next gen, and was never on a par with handling.
However, it can be expensive to fix - especially at the dealer. Here the Saab dealership shares space with Cadillac and dealing with GRM folk is not their specialty - they want $60 to replace a headlight bulb. Over the years, I did almost all repair work myself but was also fortunate to find a local independent saab mechanic. I think this is pretty crucial to a good saab owning experience. Also, saabnet.com has good support, & parts are actually quite reasonable from eeuroparts.com and others. Most body parts are shared with basic 9-3s, many engine parts are shared with 9-5s. If you are reasonably mechanically minded and have a local guy too, I think you will be fine. Check the marque boards for common problems, just like you would for any other car purchase, and so some basic research.
I miss the Viggen, and am very glad I had the chance to own it. It was a torque monster, and always gave me a reason to smile when the turbo spooled up in 2nd gear (1st is electronically torque limited) and I surprised more than a few cars in the time I had it. Going forward, I'm not sure I would buy another mostly because I really like RWD, but the experience of owning it has made it difficult to imagine what will eventually replace it as none of us want to step back performance-wise.
Start throwing $30k at the problem and many solutions appear, but try to replicate the Viggen's capabilities for $10k or less . . . I think that is tough. Sure you can get the basic performance for that $$s, but try to also get (for instance) heated leather seats with memory, 30+ mpg highway, and auto climate control. Overall, the Viggen has a pretty unique blend of executive comfort, performance, panache, utility, & economy.