I thought the similarities in structure between OTBOA and Pull Me Under were obvious from the first listen, but they're both great songs and different enough that it bothers me not.
As for the rest of the album the only other similarity I'm even vaguely aware of is the intro of Breaking All Illusions vs. that of Learning To Live.
Now, IIRC from certain interviews that occurred in the first year after MP quit, it sounded like the material written for WDADU and I&W was typically worked up by a combination of JP, KM and JM at leisure and only when they had at least an outline of a song was it introduced to MP+singer for their input. From Awake onwards much more of the writing was done in a rehearsal space with the whole band (or at least everyone bar the singer) present.
I wouldn't be surprised, therefore, if any similarities between I&W and ADTOE came about as a natural result of returning to how they used to write in the early days. Or maybe it's just that MP was the only one who was forever trying to avoid repeating themselves in terms of structures.
That said...
It really doesn't bother me at all. I assume you guys know those short making of-documentaries for SDOIT and SFAM recorded at BearTracks? In both of them Mike Portnoy shows a line of cd's he truthfully enough calls the inspiration corner. Dream Theater didn't copy Images & Words, but they might've used it in the same way that they used some of the cd's in the inspiration corner back then.
...whilst I'd like to believe inspiration corner has been done away with now MP is out of the band, I wouldn't be surprised if I&W was an album they all had a listen to around that time for one reason or another and it did indeed influence their songwriting choices.