Lack of VVT means the 2.0 will take to the turbo better. The 2.0's also lighter and has less overall options (meaning its actual curb weight is closer to its actual weight).
Usually curb weight is taken before options are slapped on the car. All that body cladding, moonroofs, side airbags, leather, etc etc...adds a few hundred lbs on top of the car's overall curb weight.
A 3i comes in at 2696 (in MTX trim)
a 3s comes in at 2762 (in MTX trim).
Not much? Neither is the horsepower difference between the two models. The 3i does have a slightly higher compression ratio (10.0:1 vs 9.7:1) vs the 3s, but thats not as important as the lack of VVT.
Most people who are doing turbo kit's aren't doing cams...the work is too expensive. Thus VVT will play a part in the effectiveness of the turbo, and if you follow miata threads...its best disabled if your boosting.
There are new exhaust manifolds. (Draxas). Didn't hear anything about the intake manifold as the stock one is pretty farking efficent at what it does. Going to a new manifold would reduce your low end torque pretty good (cause it would remove the whole cool tumble/variable manifold system).