Yes, there were way too many imo, but I liked their designs for the most part. Like I said, Manaphy should be scrapped in favor of Phione and just get a stat + learnset swap, but Heatran was a bit meh too. I don't get why they made it 50/50 for male or female though. XD I used to catch female Heatran only for lolz. The other legendaries I felt were designed well, however when comparing Dialga and Palkia to Zekrom and Reshiram, I feel that they fall flat. Dialga and Palkia were a bit overdone in my opinion.
Darkrai is perfect and flawless in every way. <3 I like both Shaymin formes, though I wouldn't have minded if we just got Skymin instead of land forme Shaymin. I don't think both formes are necessary. At least Giratina's other forme makes sense.
The Lake Trio was okay. They look too similar imo, but they're not awful. Cresselia was neat. And I think Arceus looks pretty cool too.
-wipes forehead- I think I covered them all. ~_~