Harmony remote generally have crap layouts, that's for sure. Dedicated page buttons? Ridiculous.
But having dedicated color buttons is generally lame as well today, since they were originally for teletext. Now used by some cable companies, the will usually have a specific functionality attached to them, that might be better implemented on another button. EDIT: Or functionality that can be achieved through on-screen navigation/UI (as is the case for some Sky features)
It's a shame that they're used at all since they're a usability nightmare - colorblindness, no indication of function, etc.
But lack of the colored buttons is the least of the concerns with that fugly Harmony.
A bit slow and I will have TV on whilst using the laptop frequently. I guess most here would use their laptop or tablet for a lot of smart TV functionality.
The only correct way to do smart TV is with IP control, so you can use the tools you mentioned above.