Hopefully though, the rise of MOSS compliant payment processors should make the system easier to follow - you just put a disclaimer up that final price will be based on the buyers VAT rate, and let the payment processor calculate the right rate and store the records.
Which is, of course, contrary to consumer protection laws in much of Europe. Merchants are often required by law to show tax-inclusive prices for B2C sales. (For anyone interested: I have now received conflicting advice on this from official sources in my own government, indicating that X+VAT pricing is now magically acceptable for this purpose again, despite it largely defeating the point of the previous consumer protection rule by hiding the bottom-line price in early advertising.)
The big problem with the new VAT rules isn't the principle of charging in each customer's home nation, if that just means looking up the rate for a given country from a database instead of using a fixed rate. It's a mild inconvenience, but it's an hour or two of programming work for someone, and with MOSS it's maybe an extra hour to file an additional tax return once per quarter.
For a lot of merchants (though certainly not all and particularly not the really tiny ones) the problem isn't even the need to impose VAT on transactions instead of having a threshold. As I understand it, some businesses selling digital goods in EU states didn't have VAT thresholds before anyway, so they already had reporting requirements here, and in places like the UK that did have a minimum threshold before VAT was compulsory, some merchants would have chosen to register for VAT voluntarily anyway because it was advantageous in terms of reclaiming VAT on their expenses.
IMHO the largest and most enduring problems with the new VAT rules are actually all the other things that came along with charging at customer-local rates, from conflicts with pre-existing laws on things like consumer protection and data protection (or potential conflicts, with inconsistent advice coming even from government departments) to the fact that you also have to match the entire VAT regime in each country not just the rate, which means things like knowing which rates apply to which products or services and the local geographical issues (I hope you're not just looking up a tax rate by ISO country code like, you know, everyone, because that doesn't actually work reliably). And of course you require a standard of evidence for the customer's location that will be literally impossible for many small merchants to comply with; at present, I don't see how it's possible for any fully automated system to be 100% reliable here, even for big payment services with dedicated resources and access to all the relevant raw data, because of those local issues of different interpretations of which product/service types get which tax rates and the local geographical anomalies.
The best part of all is that even the EU didn't manage to publish an accurate source of current VAT rates across all affected states in time for the deadline. The information on their own web site was actually wrong for several weeks after the switchover, because Luxembourg changed their VAT rate on the same day. And no-one wanted the data in an actually useful form so you could do something stupid like importing it into a database, right? PDFs running to dozens of pages that you can scan for relevant information are so much more useful.
Hilariously, Luxembourg are actually being compensated by the EU for these changes anyway, so all the arguments about preventing exploitation of low tax rates by different nations within the EU doesn't look so noble any more either.