Stupid for Crossrail not to serve T5? No argument from me on that, but (according to current published plan) it won't. That is not to say it couldn't change - no technical reason why the trains can't run through. It's all dependent on what access agreement can be agreed between tfl and Heathrow Airport (who own all the rail infrastructure west of the junction off the GWR line).
No station at LCY? The airport owners didn't offer any money towards construction. Contrast Canary Wharf, who funded and built the station there.