You get people like that trying to do rediculous shit with anything, it's no reason to hate on the sapiants.
Naga with Railguns: That was right after Run Faster was released, before people who hadn't played 4th edition knew they didn't have arms. Seriously, actually read the description, it makes NO mention of the fact that Nagas lack arms. And before you argue back, most depictions of Nagas include arms, so without prior knowledge or adequate descriptions it's a logical assumption to make.
Pxies with guns because they're bigger than the character: OK this is really starting to piss me off. It says right there in the shadow talk that they can, so fucking GET OVER IT! Yes it's obvious theyre going to need to be heavily modified, we just want to know the rules for getting them modified. "But, but recoil!": Pixies are inherantly magical beings, again, get over it... they fly via magic not aerodynamics, so pehaps part of training for them is learnjng how to manipulate the energy and forces keeping them jn the air to compensate for recoil.
Shapeshifters with science degrees: Yes they are animals, magical animals with metahuman levels of intelligance. Is it likely they would get a science degree? No, but simply because most wouldn't see the point not because they're mentally incapable of it.
As for why they are there... why not? Shadowrun isn't just cyberpunk... it's a cyberpunk rave party where high fantasy has gate crashed. You know why I like the ideas of pixie or centaur or shapeshifter characters? Because they DON'T fit in a cyberpunk setting, you take this stuff out of high fantasy and you have them trying to work out what the hell to do in a cyberpunk world.
I like the idea of playing a shifter who's struggling to understand the human world and turns to running to make ends meet and keep their identity hidden. Alas shapeshifters still have a bunch of holes in their rules.
I like the idea of a flamboyant pixie mage with LED hair, cybereyes and nano-tats flinging flashy illusions and roiling fireballs with equal glee. Alas weve no idea if a pixie can use augments at all, and of course backup weapons become a problem as once again we're vaguely told heavy modification is necassary but given no actual hard crunch to work with.
As for Nagas, yeah can't really wrap my head around them... but again part of that is lack of hard crunch abour what they can and can't do... at least Hard Targets gave them a venomous bite.
tldr: Shadowrun isn't just what you think of it, so get over it.