It is a hard choice. Here are a few things that I had to weigh before I chose the EVO3D
1. Photon's peripheral.
The Photon will have more available (mouse, keyboard, laptop dock), and Moto also seems to be better at getting them out in a timely manner. Moto also has dedicated HDMI port that alleviates the issue of finding a USB HDMI cable thingy (or you might already have one from other devices).
2. Photon's Tegra 2 and Playstation Suite
After the Experia Play, the next batch of phones that will be able to play PS Suite games are required to have the Tegra 2 (this may change but probably not before a hardware cycle and I will have a newer phone than either of the two). The counterpoint to this is that 3D gaming is pretty cool (there is an entire hand held based on it).
3. HTC hardware
I'm not knocking Moto's build quality however, I like HTC phones. I like the shape, size and touch (I think Samsung phones feel cheap). I also wanted to give a phone with a dedicated camera button a try. 3D was an after thought but I have found it to be better than expected and a nice feature. I don't like the look of the Photon. I can't fully explain it other than the rounded corners, I can't place my finger on it. I do miss the kick stand (Photon has one) but I'm in the process of trying to fix that without a case. The other big hardware difference is camera and I'm satisfied with my EVO3D's. Again I haven't tried out the Photon's but the pure megapixle difference can mean very little (I have a DSLR if I need to put on my photog big boy pants).
4. EVO's projected development community support.
This is still up in the air but I picked the EVO3D. This is what matters to me. I don't make very many calls, I don't rely on my phone for business and there are very few things that I own that are not modified in some way. I had immense fun with the WebOS development community and my Pre. I was happy to find an equally dedicated and brilliant community behind the EVO4G and I am betting that the EVO3D will have a similar experience.
I don't think either phone can be considered a bad choice. I have no experience with blur or much of what Moto does. In my case it didn't hurt that the EVO3D came out first but I'm pretty sure I would have waited if their release dates had been swapped. Not really a deffinitive answer from me but I'm also trying to stay objective. These were just some things I considered before I put my pre-order in for my EVO3D. Camera/kickstand/sense/blur/rooting(CM) will take a different precedence to different people.