For this reason it is hard for me to justify calling the moto X a flagship device, regardless of how much i love it because i dont think it has the build quality of an HTC One nor the specs of a GS4 but it does have some awesome marquee features and i guess some marketing. Just my opinion.
So the HTC One and Samsung Galaxy S4 are flagships and the Moto X is not because of build quality? Please do elaborate, because I've seen a lot of complaints about build quality on the former two (buttons loose, compressed, sharp edges, screens bent, screens breaking, usb ports loose, usb ports breaking, etc, etc), and a whole lot of praise for the build quality of the Moto X, with the latter being compared to the iPhone in both quality of engineering design and manufacturering integrity.
Here's my basic argument on specs:
They don't matter anywhere near as much as how well the hardware and software teams execute.
If you mean build materials, you're right, it's not made out of metal like the One, which is good because that offers up the customization options, the better feel and device balance that they created and makes repairability a much easier undertaking.
As far as specs, I wouldn't get too hung up on the sheet alone, because the S4 being the highest "spec'd" device of the three you mentioned, by virtue of having a larger number of cores and less efficient processor and a larger screen, is getting soundly beaten by smarter engineering by several OEM's. By the unofficial top ten list stanards (bunch of nerds evaluating devices, not based on sales), the One is still hanging on to it's top 5 device postition 6 months in, the Moto X is making a strong top 3 showing, the iPhone 5s (another dual core powerhouse) is top 3... but the S4 is barely in the top 10 (it is #10). Samsung remains a top player with 3 devices in the top 10. Not everyone agrees with the exact order of the top 10 list obviously, but the trend is still pretty clear: Care and design are being valued highly, as well as performance. The S4's sole factor of greatness for 2013 was it's camera, which is one of the best in the Android world.
As far as defining a flagship... if your company releases one phone per year, that's your flagship. Varients on a theme, it's the stunner of the bunch. HTC obviously the One. Moto, obviously the X. Nexus, obviously the 5. Apple, obviously the 5s. LG has an interesting situation that could make it OEM of the year, having had 3 separate devices in the top 10 for a couple months now, 2 solidly in the top 5 (Nexus, G2 and G Pro).
Devices aren't generally objectively better or worse than other flagships across the board, there's always the all important question of, "at what?" to ask. Camera, get a samsung or an apple. Blazing software and resistence to obsolecence, get a Nexus.... etc. Different strokes, that's why we like choices.