We use T-Slotted extrusions for a low volume benchtop product and have had a number of issues; I won't name the manufacturers as I'm fairly certain that they don't supply the US market. The only approach to standardisation I've encountered is the section size and T-Slot width; the slot profiles and hence the nuts vary, even with the same manufacturer, where the thickness of the top of the slot is different on the same sections, according to whether light or medium duty.
The main deciding factor for us, was that we wanted a neat Butt-joint between the Vertical and horizontal members of a visible frame; so we chose one that did both 45mm and 40mm sections, this meant that the smaller section of the horizontals sat square on the face of the larger verticals, between the adjacent corner radii. Whereas, had they both been the same size, it would have left an ugly dirt-trap (I hope you can follow that)!
The issues we encountered and important things to consider are as follows.
1/ Surface finish, will it be visible? If so, the finish needs to be consistantly good and free from scratches and dents, this is much more important if it's for a finished product that you want to put your name on, than if it's for a storage rack! There's very little that you can do with a damaged anodised surface that won't make it look worse!
2/ Will you get them to supply it cut to length and how accurately can they do it? The first few batches we got were done on their brand new CNC saw and were brilliant, but then the blade was replaced (or badly re-sharpened) and it started pushing off, so it was no longer square and the lengths varied. If you do need it to be accurate and square, and especially if you need to do any machine work on it yourself as we did, then get it a little longer and finish the ends square and to length yoursef when you do the machining. It will be cheaper if you can relax the cutting/squareness tolerances, you're in control of vital sizes and YOU can take care to keep the vise jaws clean and not to embed swarf into the visible faces (Arghh)!
3/ Finally, choose a system that has well designed and rigid brackets and a clever method of joining the elements, preferbly something that "Pulls" the faces together and just doesn't rely on the friction of grub screws, which will surely open up in use (if not on tightening and handling)!