The advantage of the supercharger is that you can remove it and sell it when you're done with the car. You can't say that about a bunch of cheaper bolt-ons.
If you had 50k miles on the car and were going to keep it for 10 years, I'd say build it up. Otherwise, I'd just bolt on a blower and enjoy it with the deficiencies (such as traction, driveline wear, etc.) If stuff breaks while you still care, fix it. If it holds up, even better.
The last thing you want to do is dump a bunch of dollars into the car, which you'll never recoup (you're likely to get less than half of what you paid for the blower, assuming you remove it the right way, but that still beats getting nothing for bolt-ons.)
I sold my PI Headswapped '98 GT for the same price as every other GT for sale at the time. Mods put no premium on a car's resale value. Just don't go nuts with the boost and you shouldn't require a costly tune to enjoy it (now to extract the most power, that's a different story.)
SOLD: PI Headed '98 GT - 248rwhp/306rwtq - email@example.com (2.0 60ft 3300+ DA)
'11 TDI Sportwagen - 50 mpg Daily Driver - Not Quick.