I run both - software and hardware. I do 98% in the Elk and 2% in Elve... the stuff Elk doesn't do as well.
One reason for the elk that's nice is that anything the Elk controls, so does anything else that controls the Elk... meaning if I want iPhone control, I buy eKeypad and now have access to my Elk and everything connected to it with 2 minutes of configuration; keypads, HVAC, lighting, sprinklers, garage doors, etc. Same on the PC - fire up ElkRM or M1toGo and I have access to everything.
Behind the scenes, I also have Elve running so I can someday toss in some customized touchscreens and also to run rules in the background.
I use a PIM on both systems so each has direct access to lighting - there are some advantages especially when using Elk/UPB. Each can use the lighting controls natively.
If you don't need all that or you need to save money, getting a DSC or somethign the ISY supports may be an option too, but check closely to see what each can control to make sure that rules that cross between devices are easy enough to program.
To expand on the automatic lights - I do that too; on alarm, all lights on or flashing (depending on arm status/type); when opening a door while alarm is armed and it's dark, light a path into the house; arm house, all lights off at end of countdown timer... plus a step further; non-alarm zone contacts on a few doors in the house - in hall closet, turns light on/off; on young kids' doors - alerts us if kids are leaving their rooms in the middle of the night, and also turns on the bathroom lights for them at a dim level, and turns them off when they go back to bed... it works really well and provides extra piece of mind.