Yes, it's never quite been as popular as when the fad was huge in the gen 1 days (Red and Blue sold 23-25 million, compared to about 18 million even for Gold and Silver), but since then, sales seem to have been declining quite a bit:
Ruby and Sapphire: 16.22 million
Diamond and Pearl: 17.63 million
Black and White: 15.58 million
Black and White 2: 7.81 million
Pokemon X and Y: 13.29 million
It's not a huge decline, but it still seems to be a steady decline in sales, and I wonder whether anything gameplay related might be responsible (like how Zelda's been losing sales since about Twilight Princess).
I'm sure all game sales do that. I'm willing to bet the sales of Mario has gone down too. Same with Call of Duty, Halo, everything. No matter how popular a series is, sales usually go down.
I'd guess that Mega Evolutions lost them a chunk of those fans…I know I seriously considered if I was going to keep playing the games when I learned about them. However, on the whole, I think that the decline in sales has to do with the fact the 3DS lost some fans because of the 3D aspect (despite the fact you can turn it off, which is why I always thought that argument was completely groundless). It would also help explain decline in Zelda sales since TP (SS's controls being wonky, N64 remakes and LBW on 3DS, and then another remake on Wii U, which typically implies lower sales than when it was original). I'd guess those factor in more than a blatant loss in popularity…dislike of the direction its heading is certainly in that category, but dislike of the hardware it's on doesn't qualify.
Well, it took them a long time to decide to improve the graphics, and finally move into having 3D battles. There are a lot of things they could do to reinvigorate the series, like new Pokemon Stadium and Snap, which have loooooong been asked for. All they have to do is make the same game, with new, glorious HD graphics, and all of the new Pokemon and they'd be set. Instead they keep inundating us with the Rumble games (Which are cute, but nichey) and the Trozei style games. Pushing F2P isn't likely to endear it to many fans either...
If we get Pokken tournament soon, and they pull their heads out of the back ends on making a new Stadium and Snap, some games that'd appeal to a more adult fanbase as well, they'd probably see an improvement in the series sales... Games like that might help to remind fans that, oh yeah, I really like Pokemon! Would help give them a signal boost when the new one released.
Popularity has declined since the original came out, but it seems to have been pretty consistent since the DS days. Diamond and Pearl sold 17 million units to 140+ million DS owners before B&W came out. Historically, 2nd acts never sell as well for Pokemon. RB>GS, RS>FRLG, DP>B(2)W(2), XY>ORAS.
Red and Blue sold 31 million units to a total 118 million GB owners. About 1 in every 4 owners had Red or Blue.
Ruby and Sapphire sold 16 million to a total 81 million GBA owners. About 1 in every 5 GBA owners.
Diamond and Pearl sold 17 million units to a total 154 million DS owners. So about 1 in every 9 DS owners.
X and Y sold 13 million to a total of 52 million 3DS owners. About 1 in every 4.
The ratios seem to stick around the same except for Diamond and Pearl, but that is probably due to two things: the massive success it had in the casual market (Brain Training, Nintendogs, etc), and the plethora of Pokemon games on the system. We had 2 generations on the DS as well as remakes.
Sales might be declining but that seems to be more correlated with system sales rather than popularity. We are getting Pokemon movies churned out on a regular basis now and the anime is still going strong. I still see plenty of toys for it at stores too.