Previous large-capacity Aprilia engines were either made by Rotax or made under contract by Rotax. The build quality was always top-notch. Now Aprilia has their own designs and production but they seem to have continued the high-quality design ethos.
They have had a few issues - the maintenance requirements are stringent, which has caused a bit of a bad rep for their 450/550 V-twin in the US when people treated them like Japanese engines - i.e, never maintained them. But I have found them to be pretty damned good - I am on my 6th Aprilia now and apart from a self-destructed sprague clutch on my Futura (cheap buy - I knew the previous owner was an abuser
) they have been great on reliability and performance. Easily tuned as well.
The V4 is rumoured (I haven't found corroboration from Aprilia) to have been the basis for a GP engine in the 990 era so the chance that the engineering is of a higher standard than the road-oriented Honda is probably quite good.
I think the market segments are different. People expect trouble-free operation from Honda, so the design is based around surviving abuse, whereas Aprilia expect their owners to maintain them to the recommended service intervals by trained technicians (like BMW in that regard). They have been sticklers on warranty - if you haven't got the right stamps, you are on your own.
To work on, they are like chalk and cheese - Aprilias are easy - getting to major components is a breeze compared to something like a VF800, where you need to just about disassemble the whole bike to get at stuff.
That being said, I have never had my hands dirty on the Aprilia V4, but I know plenty of people that have and the rep seems to be the same.