Sales might not be indicative of the anime’s popularity, as understood by those who watch anime regularly.
E.g. if asked what were the best animes that you watched, what most otaku would say.
First of all, there’s a large number of people which only stay in the anime for 1-2 years (and even more who only watch less than 10 series). They will vote for Shingeki no Kyoujin because that’s what they watched and it was good. But if you watched anime for the last 10 years, you wouldn’t necessarily say Kyoujin was the best that you’ve seen (even though it’s OK).
So even other reasons aside, sales mostly show “what was hip at the time it came out”, not “what was etched into the hearts of long-time fans the most”.
Now, if you look at the list, there’s only Gundam SEED in the top 10 which can’t be considered relatively modern (let’s say modern era starts with 2006 Haruhi / Geass). There’s only SEED, FMP and Initial D in the top 30!
Even if you count “Modern” from 2009 / Bake, there’s only SEED, 00, Macross F, Geass, Haruhi, FMP, Lucky Star and Initial D (10 slots total) which haven’t been made in the last 5 years.
Modern animes are disproportionately present in the top sale charts.
It’s not that anime has gotten just that much better. Delivery prices, channels and anime popularity vary. Perhaps anime DVDs cost more or weren’t as widely available, or it wasn’t as common at the time to buy them, or economy was worse, or anime in general had less fanbase.
Recent animes also have a better potential fanbase. Older otaku may still vote for them, while younger otaku will not, in general, watch lots of older animes, and even if they do, there’s usually no way to buy one (increasing the sales).
In other words:
most popular != the best.