It kind of depends on what time frame you are modeling your Big E for - mine was for a 2005 deployment, where I needed EA-6B Prowlers. The clear canopies were worth it to me to get the gold-toned effect they have (which lookes pretty cool from certain angles); plus, I think the Trumpeter aircraft have a little crisper molding and I hand painted all the ones for my build anyway (no canopy masking!). If you're going to use F/A-18C Hornets, look for the old Fujimi set (cheaper than Trumpeter and has some small deck tractors included).
As far as PE goes, the Gold Medal Models supercarrier set is outstanding; if you want to add 8-bladed props to your Hawkeyes, the 1/700 aircraft bits fret from White Ensign Models can provide the necessary props and some other helpful bits.