I haven't noticed EPUB suffers from bad support. I like its principle (just a markup language), the two problems I came to see: 1) handling images, tables... objects that may need to be cut are cut at the expense of the ease of reading. And 2) no handwritten annotations.

But you're right: deep down, both depend on the implementation, not on the format itself so you could actually blame the support. (Yes, I somehow changed my mind in the process of writing this comment.)

I don't know about EPUBs support too much, my only experience was with Apple's iBooks, which (in most cases) handled EPUB ebooks very nicely (display-wise) with well formated, colored code and ect.