potato/potato.
With the APR changes and emisssions crack downs, id probably go Uni to futureproof the next round of mods/tune... but thats just me.
I'm not sure what you're referring to exactly because I believe all companies are being subjected to finer restrictions with regards to what products they put out and how that effects emmissions. APR was probably targeted first because they're one of the largest and well known but at the same time, I think they've already dealt with it. They're removed various products dealing with emissions including tunes off their store.
Since Stg1 requires zero additional hardware, I don't see how that would ever be touched. My local VW dealer still distributes their tunes... If when you say future proof, you mean that, if you went Stg1 now, you might not be able to go Stg2 in the future, then I can see your point there. It depends on what route they want to go.
Personally, if my turbo ever blows, knowing APR has a IS38 tune using stock downpipe, that would just be my next route. No way will I deal with the hassle of down pipe for a few more ponies to go Stg2... Ultimately I feel that bringing a downpipe into play and the tunes that require one are the ones that are most likely to be brought/taken down.