Yeah, these All Time polls always fluctuate wildly based on what's in vogue at the time. For instance a quick Googlin' reveals these were their best games picks in 2010:
01. Final Fantasy XIII
02. Dragon Quest IX
03. Monster Hunter Portable 2nd G
04. Final Fantasy X
05. Tales of Vesperia
06. Metal Gear Solid 4: Guns of the Patriots
07. Persona 4
08. Final Fantasy VII
09. Tales of Graces
10. Yakuza 3
It's not specifically an RPGs list, but RPGs dominate these lists anyway. Here's their picks in 2006, which at least all seem to lack the flavour of the month picks:
01. Final Fantasy X
02. Final Fantasy VII
03. Dragon Quest III
04. Dragon Quest VIII
05. Final Fantasy IV
06. Tactics Ogre
07. Final Fantasy III
08. Dragon Quest VII
09. Dragon Quest V
10. Far East of Eden 2
Final Fantasy VII is the only game that appears on all three of these Famitsu "best of all time" lists. Of all the games in the OP, only Chrono Trigger and Suikoden II are franchises that have no active buzz. I wouldn't read into it too much.