I know, the devs won't like me for this one, but i still hate how wonky channel management is. I wish one of these would be fixed.
Favorites:
Famously don't sync, unless you nuke the client (and for those using betas, nuke beta and live clients)
Otherwise, they work great, as they do keep in-line with HDHR favorites. If only they synced with the clients.
Channel collections:
Don't respect the client guide channel order. I just want a list of channels to match what i want in the client, and let the client sort them that way. I shouldn't need to sort on the WebUI every time i add a channel, or collection. Trying to jury-rig the channel order on the WebUI, especially the first time, is needlessly difficult.