Pokemon Platinum. Remains best in the series to this day. Untouchable post-game.
There were a lot of games that I considered contenders back in this year but thinking back I don't really consider them 2009 releases. For example I imported Pokemon SoulSilver by the year's end but that's a 2010 game to me now. I thought about giving GotY to Sonic's Ultimate Genesis Collection, which is still the best game collection to this date, but that's kind of cheating. And then that year I did give it to SoulCalibur: Broken Destiny, which is more or less a modified port of 4's engine for the PSP and probably my favorite in the series content wise, but these days I don't care much about fighting games for single-player so it's kind of useless.
There was also Fire Emblem: Shadow Dragon, which I straight-up loved on first playthrough though on a subsequent one it was apparent I only really liked it a lot in the first place because I forgot how great the rest of the series was in comparison somehow. My LTTP would go to Beatmania IIDX 16: Empress, which is a fantastic farewell to console-released Beatmania games.
There was also a lot of great stuff that year that I didn't mention that wasn't really a contender. Star Ocean: the Last Hope (screw the haters I liked it, that battle system was incredible), Halo 3: ODST, Wii Sports Resort, Pokemon Mystery Dungeon: Explorers of Sky, Final Fantasy IV; the After Years, and BlazBlue.
This was kind of a weak year for me coming off 2005-2008 and probably one of the weakest of the decade overall (second to only 2002), but at the time I was still catching up on old stuff for the most part (and playing a shit ton of Rock Band 2, especially with all the DLC releasing that year), so I didn't really mind, and for my personal gaming experience this might have been my most active year ever. I don't think things really sunk in as having been worse than 2005-2008 for me until the subsequent year 2010, which was actually a somewhat solid year.