Bolded I dissagree.
Italics I agree.
Some of the pokemon you have mentioned are actually quite useful, it makes me think you haven't actually had much experience using them. But that's just a guess. XD Gyarados is a great pokemon, but I think it should be Water/Dragon instead of Water/Flying like you mentioned. When I found out I was like wtf! D:
OK let me add some explanations...
Rattata, Raticate, Seel, Dewgong, Krabby, Kingler, Goldeen, Seaking, Furret, Noctowl, Qwilfish, Teddiursa, Ursaring, Swinub, Piloswine, Remoraid, Octillery, Stantler, Linoone, Silicoon, Beautifly, Taillow, Swellow, Skitty, Delicatty, Volbeat, Illumise, Grumpig, Clamperl, Starly, Staravia, Staraptor, Kricketot, Kricketune, Boneary, Lopunny, Hippopotas, Hippowdon, Finneon, Lumineon - Utterly uninspired. These are animals, not Pokemon.
Golbat - Unnecessary - should go straight from Zubat to Crobat. I don't like the way they gave it eyes and a ridiculously large mouth.
Voltorb, Electrode - Stupid. I like the idea of them disguising themselves as Pokeballs but how do they move? They must have some sort of ghost inside them, in which case they should be of the ghost type.
Exeggcute - No means of propelling itself. I love Exeggcutor though, so maybe I'm being a bit harsh. It's just that most Pokemon lay eggs and I find it weird that these ones fight in battle... how exactly?
Omastar - It should exist but it's just not good enough for me. Not nearly as good as the other ancient Pokemon.
Lanturn - I just don't like it. I liked it's prevolution but I feel that they should have given it more lights or something rather than making it into a dolphin with the same lights.
Cleffa, Igglybuff, Wynaut, Bonsly, Mime Jr., Happiny, Mantyke - Stupid baby Pokemon. The real babies are Charmander/Bulbasaur; at least they have something about them and aren't virtually useless and copies of each other.
Flaafy - I don't get why it's pink when the other two are yellow.
Bellossom, Politoed - Makes no sense that they're related to the other guys.
Sudowoodo - I just don't like this one.
Hoppip, Skiploom, Jumpluff - I just don't feel that there's much of a progression, it's just like three copies of the same Pokemon. And just because they're light and can jump around like they're on the moon, doesn't mean they should be flying types.
Sunkern, Sunflora - Uninspired, plants not Pokemon.
Wooper, Quagsire - Hmm. I've changed my mind. They're alright.
Misdreavus - Too much like the head of a woman. Raises lots of philosophical questions about whether people living in Pokemon land can turn into Pokemon after a horrific death or something.
Unown - I just think it's a really stupid concept and design.
Girafarig - As above. What is that thing on its tail? Just weird.
Dunsparce - Self explanatory.
Porygon 2 - In what way is it better than the ordinary Porygon? One would think that in the Pokemon world, after the creations of Mewtwo, they would have realised that it's a bad idea to keep trying to create Pokemon.
Tyrogue - Ugliest Pokemon ever.
Blissey - Just makes you feel bad for Chansey. Why would you have a Chansey working as a nurse for you when you can have a Blissey?
Masquerain, Mawile, Chimecho, Snorunt, Deoxys, Burmy, Wormadam, Cherubi, Cherrim, Chingling, Bronzor, Bronzong, Spiritomb, Frosglass, Uxie, Mespirit, Azelf, Dialga, Palkia - I can't work out what these are supposed to be. Digimon?
Shroomish, Breloom, Nincanda, Nosepass, Barboach, Whiscash - Ugly.
Plusle, Minun - Eurgghhh I hate Pikachu copies and I hate 'two for the price of one' Pokemon. Waste of space in the Pokedex.
Vibrava, Flygon - I think they only made these because Yanma was such a failure.
Castform - Nice idea but not very good at the end of the day.
Shuppet - Banette is suffice on its own.
Beldum, Metang, Metagross, Regirock, Regice, Registeel - Digimon.
Latias, Latios - Should evole from Togetic.
Jirachi - Legendary for the sake of being legendary. And how is it steel type?
Luxio - Pointless middle ground.
Budew, Roserade - Just a copy of that other one that has flowers.
Pachirishu - This is a squirrel Pikachu.
Magnezone, Lickilicky, Rhyperior, Magmortar, Togekiss, Yanmega, Dusknoir - I think the only reason these exist is because they didn't make the prevolutions strong enough. And so they ended up making them look ridiculously over-elaborate instead.
Glaceon - I think they took the evee-lutions too far here.
Porygon-Z - Now they're just taking the piss.
Gallade - It's a feminine Pokemon. Just let it be. This is like making a male version of Jynx or a female version of Tauros.
Phione, Manaphy, Shaymin - There's nothing legendary about them as far as I can see.
Darkrai - I just don't like it. Digimon style design... hasn't really got anything uniquely interesting about it... certainly doesn't stand out as legendary... doesn't make sense that it's the dark type and not the ghost type...
Arceus - I just think it's over the top.