There's a few things to think about here:
Are you using a lot of memory on textures already?
If you make all your texture rect sizes uniform (rects being the slice of the texture that represents a single frame of animation) and draw them all on the same size quad, are you drawing a lot of transparent pixels to the point where it's taking too long to render a frame? (more problematic on mobiles)
Are your art assets already in one format or the other?
Is it easy for whoever is creating your art to do one way versus the other?
The advantage of uniform rect sizes is that they're stupid-easy to deal with in code, and may or may not be easy to deal with from an art perspective. Some artists work by default drawing their sprites such that the character is already centered. This is less efficient both in terms of memory and (potentially) in terms of what you're making the GPU render, but before you start worrying about that you need to identify that this is even causing a problem for you.
Real world examples:
I've worked on a couple of 2D projects recently where each used a different approach.
The first had an isometric view, so our artist was modelling and animating characters in Maya then exporting them as a series of PNGs. Instead of making him pack together his own sprite sheet, I used a sprite packing tool that automatically generated frame positions and dimensions for each frame of the animation that he exported.
The second project was a platformer and our artist was animating each frame by hand. After doing a rough sketch of each frame in a character's animation, he would lay out a sheet in photoshop and draw directly on that. With this setup we figured that re-packing the sprite frames would have just been a waste of time. Thus we used the other approach where we just divided the spritesheet evenly in code and identified each frame by a single index.
This also enabled us to make a fun little animation file parser that let you easily mix and match animation frames. It's very possible to do with packed sprites, but I would have had to put a little more brainergy into making it happen.
Here's what the animation files looked like:
# Texture filename
# Frames across,down
# Basic Animations
# Special animations made out of frames from animations above