Lag is a real problem with this type of mods. They are built around the idea that you need to automate as much as possible and scale things up to progress at a reasonable pace, and while there's nothing wrong with the idea, minecraft just can't handle it. If you pay attention and use the most efficient (hardware-wise) way to gets things done you can get a bit further, but the game will always get worse.
In my play through I built a void base with everything on it's island and ender chests/tank to move items around; my laptop initially seemed to cope with it well but as I progressed in some areas the FPS would start dropping, and there isn't all that much.
I tried GT:NH just to see how my computer would handle it: on a fresh world I get around 20 FPS with spikes, NEI takes about 5 seconds to update after I type something and if i go near one of those underground dungeons the FPS don't go above 5.
While GT:NH isn't the best example since it's a very big modpack, it gives an idea on how things can get. The only solution I know is having a real beefy computer, and even then i don't know how much it helps. Either that or enduring the lag.