Four things jump into mind when comparing the E55's vs. the E5's and that's increased bass, increased dynamics, higher sensitivity and lower distortion. If you can get the bookshelve(s) within a close distance of your sub(s) then it will act as a single speaker and you wont have issues (bass muddying the midrange since they're 2 separate enclosures), but that point is null since the E55 tower has a separate compartment for the tweeter/midrange. Lower distortion throughout the midrange and bass should be present obviously. The tower speaker will definitely hold it's composure more at higher SPL's.
I think within a certain price range a bookshelf + sub setup is better than a tower setup. If you already have a sub, then it becomes a little less one sided towards the bookshelves. Most towers under $5-6k or so will need a sub. No question about it. Some people might be okay with not having one, but you're missing the lower end and that's a fact. Not many towers will go down to 30hz or below with authority anywhere near that $5-6 price range. Another thought is that if you're needing stands, you have to add that cost to the bookshelf speaker cost. Sure some stands are cheap and look that way..if that's what you're wanting then that can help your decision sway towards bookshelves even more, but most don't want crummy, ugly looking stands and when dealing with this specific situation you're getting awfully close to being near the price of the towers. Larger cabinets are also more resonant than smaller cabinets (bookshelf) so there's that. In this price range, that can be a factor as enclosure quality can be subpar and color the sound. I do not believe it's an issue with the E55's. On the issue of bass, the E5 bookshelf will play down to the x-over of your SVS (I assume around 80), but it's definitely not going to be playing as cleanly as the E55....and even more so with increased volume.
I could keep going and going, but as you can see there are trade off's to each. I personally think monitors and sub(s) can be an extremely nice setup if you have a smaller-ish room, ability to place the stand mounts where you'd like (aka...no small children; this is not me!), etc. You're usually going to be able find a much nicer bookshelf than a tower when using the same budget ($1,000 tower pair vs. $1,000 bookshelf pair). Clearly the less drivers, smaller cabinet can lead to nicer drivers, more inert cabinet materials and build, less complex & nicer quality x-over, etc.
With that being said, my situation required towers more than bookshelves. I have a very large room that's open to other parts of the house, a small kiddo that I wouldn't want a speaker tipping over and knocking her in the head or smashing a finger/toe and I like to listen loud. Higher sensitivity speakers might have suited my room better, but I'm not huge on the Klipsch reference line and most other stuff that's a lot more sensitive is higher priced or a DIY type thing, which I don't have the time or products for.
Panny 65st60 / Denon X1000 / EMP e55ti / EMP e56ci / EMP e5bi / (2) e1010i