THX Select certification means that the receiver has passed a rigorous set of performance tests defined by THX and the receiver will also include THX sound fields and post-processing routines. The Denon may or may not be able to meet the same performance metrics (although many people will say they simply didn't want to pay for it). In my book, THX certification is a plus so +1 for the Marantz.
The ability to upconvert to 1080p is a 'nice to have' IF you need it, which you most likely won't. Every device under the sun nowadays can upconvert so having a receiver that can do it is only useful when you have a source device that does not (or does a poor job of it) - like some cable boxes. The TV is going to scale and deinterlace if necessary anyway, but sometimes a receiver might do a better job. I would weight video upconversion as zero when deciding between two receivers.
Practically any remote will play nice with either receiver. Since the Harmony is mostly used in a pre-programmed fashion by downloading the appropriate codes from their website, the only potential issue is that their database doesn't have all of the codes you need. As long as the remote also includes a learning feature and I think most Harmony models do, you can configure it to work everything properly.
