Until a short time ago, I didn't mind, except that now a few problems rise with the sheer amount of legendary Pokemon. The first one is that they are a pain to catch, which makes legendary battles a complete waste of time. I mean, in Gen. I, that was okay since there were only 4 legendary Pokemon, which meant that aside from the trio and Mewtwo, who was an endgame mon, you didn't have to spend so much time in catching these legendaries. Nowadays, they often tend to put 10+ in one game. Another reason is that Gamefreak does nothing to most, no interesting sidequest, nothing, they just wait in the middle of nowhere waiting for a trainer. Suicune's side-quest in Crystal was interesting, why not add similar stuff to other games. Plus, there is also the fact that several legendary Pokemon are event-only, which means you have to either be lucky with the calendar or have a gameshark in order to complete the dex.
RBY
-stationary trio
-stationary endgame uber
4
GS
-roaming trio
-stationary uber, and a second stationary uber in the postgame
4+1
RS
-stationary trio, puzzles
-stationary uber, a second stationary uber in postgame
-an extra roamer postgame
4+2
DP
-stationary/roaming trio
-stationary uber
-postgame has a roamer, second stationary uber, 2 stationary extras (one requiring transfer of legends from past games)
4+3(+1)
BW
-stationary trio
-an extra roamer
-stationary uber, a second one in postgame (and another if you manage trading the roamer counterpart)
5+1(+1)
In a simplification, not much has changed. Current gen you come across ~3 more legends in a casual playthrough than at the sole beginning of the franchise.
Note also that mascots have had their catch rates increased to 45 or something in the last few gens.
If the regular main games of the recent generation had you catch a stationary trio, a roaming trio, 6 ubers/mascots, aaaand 7 extra postgame legends, (so like 20 legendaries) I would say you have a point. But its not half as bad and pretty much like its always been.
The only serious change is the additions of ~3 event legends that are handed out to keep the generation alive for some time. And those you don't even have to actually catch most of the time.
And about
"Suicune's side-quest in Crystal was interesting, why not add similar stuff to other games."
I thought they did... adding puzzles to solve to access golems, have Groudon/Kyogre appear and escape before you later actually encounter them, having to check out the lake guardians for the spear pillar event to take place.. and I don't know whether you got a chance to play BW2 yet, but how you meet the musketeers there reminded me particularly of Suicune.