Yes, we should be able to expect to be able to reliably transfer files between applications. That's what standards are for, and EPS/PDF are both standardized formats. The problem arises when some developers don't follow the standards, which is why I tend to stick with Adobe software, since they're the ones who developed the standards in the first place.
That's actually a problem with closed source in general. They can't or won't follow standards, because they can't implement processes (or effects) the same way between programs. Or be able to implement ways to render how the other program will export those "standard" files. When they try to, they are having to retro fit it into the latest release, which won't be on parity with the latest release of the competitor's software. Or they are trying to avoid parity completely in order for market place advantage.
I have zero problem reading EPS files in Evince Reader, even though taking those same files and Ai will spit back errors or not render the same way (and I usually have a jpg file to confirm, so I know which program is rendering correctly). Bare in mind, Evince is just a reader, it isn't also try to open that file for manipulation, which is where the issues can come about, it's trying to do too much, but maybe Evince rasterizes it when it opens it. That could be a possibility, I haven't actually investigated it too much. Although, it doesn't matter to me if it does or doesn't rasterize it as I do the exact same thing to the file regardless if it's a vector or raster file. Just so long as I'm able to view it is the key thing.
Then, of course, you have some users that don't handle things on their end. I remember when gradients on strokes was available on newer programs, but people were still on the old. If the content creator didn't outline the stroke, it wouldn't render correctly to the next person. Have custom brushes (I do)? Same problem as the gradient on strokes, even more so, because that is still an issue no matter what version one has, at least with gradients on strokes would be handled in future releases. So some issues could be that there are effects being used on newer software versions that the competitor product isn't able to handle, yet anyway.
Then of course, if they exported to low of an EPS some effects were lost as well.
So it's double edge problem of developers
and users in my mind.