Clouds have a ton of issues. Most of these have been on the JIRA at some point. A few are closed. Clouds as a whole are obviously still broken unless they are intended to be ugly as all hell and not work hardly at all when handled with resource packs.

For starters, completely opaque when seen from the bottom. This has been covored and the mods here decided that it's intended to be that way because it was designed before the sky limit was raised. That suggests that there is a general incompatibility with the design of clouds and the design of the minecraft world, and that should be seen as a bug in and of itself.

Second, this causes another issue where cloud designs with a nice gradient translucency look pretty decent from the top, but have an abrupt drop off when seen from the bottom. This issue doesn't really require there to be structure above the cloud line, it's ugly either way. I really doubt someone put effort into making the clouds deal well with translucency only to let it fall apart when viewed from the side you are on 99% of play time.

Nice smooth translucency: http://i.imgur.com/fvSINqE.png
Same texture crapping out when seen from below: http://i.imgur.com/UqSERJQ.png

Next, we have the problem where the "walls" of the clouds don't come together perfectly, and that's covered. What's not covered is that when you apply a resource pack with a translucent texture for clouds, that gap gets even weirder as seen above. Cloud "walls" intersect eachother, edges resting meters apart and not even lining up with the edge of the texture according to the break noted above. This causes the most bizarre looking jagged edges to appear.

Finally, frame rates drop when clouds are in view. That's stupid. Basically this on top of the other issues mean most players just turn clouds off. If you think that's an acceptable solution then perhaps clouds should just be cut from future versions of minecraft.