I had a feeling you would - the E-1000 really isn't all that great. As for the final choice, it depends on three things - whether you have any intention to hack them, what you're going to do after hacking them and which
"poison" are you going to pick in terms of the screen.
Here's a comparison of the PSP-3000's screen and the PSP-2000's screen
(the common type). As you can see, the 3000 still ghosts and on top of that interlaces. The PSP-2000 ghosts, but the colours appear brighter and richer. Hell, if you're lucky, you might get a 2000 with one of the screens that didn't ghost at all
(there were several revisions within this family) but that you'd have to determine yourself.
As for the hacking aspect, check if the PSP has a Data Code of 8B or lower. To check that, remove the battery from the battery compartment and look for the serial number on the sticker there - the Data Code will be next to it.
The reason why you'd want to know is that 8B or lower signifies an earlier motherboard compatible with Pandora and this compatibility is desirable for tinkerers who like to modify and customize their system without the risk of bricking it - Pandora allows you to unbrick the PSP practically regardless of what you've done.
If it's above that point then chances are that the hardware will be practically identical to the PSP-3000's as far as the motherboard is concerned, in which case I recommend the PSP-3000 instead.
As for comparing the systems beyond this scope, they're about the same in terms of comfort of use. The PSP-3000 has a built-in microphone and a more common serial bus
(next to the headphone jack) so it's easier to get a remote and an external mic for it, but it's not impossible to get them for the PSP-2000 and I doubt that the microphone itself will see much use anyways as it's only used for Skype and SOCOM games, the latter of which have been taken offline as of late.
To reiterate, I would pick the PSP-2000 if it's one of the early, pre-8B ones. If it's not, PSP-3000 all the way as it simply offers the slight edge in terms of features and it's easier to get accessories for it.
I hope that I was relatively helpful in making the decision.