I wouldn't actually say that it prevented bases from being as large, so much as the AE networks themselves are going to be more compact. This isn't actually a bad thing, and it won't really impact things on the grand scale if you think about things in a slightly different light.
Bases with Fluix Cable running all over the place are probably a thing of the past. However, that doesn't necessarily mean you can't use AE to automate everything, just that it is going to be separate self-contained systems connected using some other mod.
AE2 is a much more... decentralized mod. Things can be produced locally, then exported to your main storage area. For example, let's say you have a farm that you want to automate food production from. Local produce is piped to an ME Interface which then stores the produce on disk. Then you've got an Interface with several MA's attached to it set up to auto-craft the food item of choice. As long as you have all resources local, there's no need to hook this system up to the larger system directly. Instead, you can set up an Interface to automatically provide the end-result, which then gets piped out of it and sent to your main storage area. Since you are using actual pipes to provide it, you aren't really needing to worry about it eating up channels. Total channel cost on this ad-hoc system? Well, you've got one interface, actually it can be used for both importing and exporting since it can provide the result and accept any imports, a Drive with disk for storage, an Interface for crafting, and a Terminal. Oh, and the 1k CPU for a total of 5 channels, and it produces one useful thing.
But more importantly, it doesn't eat up channels from your main system, which can use a single input interface for all peripheral local systems to input into.
What I believe was seen as an 'abuse' was DW20 using P2P tunnels to run liquids and power all over the place 'because why not'. If it is cheaper and easier to run power and fluids using AE P2P tunnels rather than running pipe... something needs to be adjusted. I believe that has been dealt with.
Now, if it could all be connected using Logistic Ducts? Mmmm... now that would be fun times.