Accepting payments from users can make the site have to deal with sales taxes or VAT in every jurisdiction that it has paid users in.
A reasonable way for sites to deal with that is for the site to not sell directly to users. Instead they sell to some third party aggregator and the aggregator sells to users. Basically the same model we see with app stores--people in 20 different countries buy your iOS app through Apple's store and it is Apple that deals with the 20 different tax authorities.
I think we'd end up with a very small of very large aggregators, because generally a bigger aggregator is more efficient than a smaller aggregator.
But then we probably won't need micropayments for this. Nearly everyone will be using the aggregators enough that an occasional normal sized payment to maintain a credit in their accounts will work.
There needs to be political will to do so, but if advertising does become unprofitable there will be pressure for such political will to exist.
Also, sales tax is mainly a US problem with every state rolling their own tax regime. Intra-EU VAT collection is actually pretty straightforward in comparison; unless someone claims to be not from EU or is an EU-based business, you charge the nominal VAT rate from your country, remit it to your government and call it a day.
Assuming you are talking about VAT MOSS, it's the VAT rate of your customer's country.
You also need to collect multiple pieces of non-contradictory location proof to justify why you are charging the rate you are.