Honestly the answer is get both...When I bought my first Jeep I had just the hardtop and I asked myself the same question. I didn't live in a great neighborhood and I was worried about harsh storms (I lived near the ocean). I bought a flip top, thinking I could either flip on questionable days and take the windows out on nicer days. I found that I put the top down more than I thought, so then I invested in the bikini/tonneau option. When I would be home for 3-4 days at a stretch I would use the bikini tonneau, other days I would just have the top up. When I bought my next Jeep I didn't bother with a hardtop at all, I just got the soft top and ordered a bikini/tonneau. I live in a better place now (altho I still don't leave any valuables in the Jeep at all) so I can leave the top down from April-October, but it's nice to have the soft top for longer highway trips and overnights in places where I'm uncertain.
Basically either of your options will work, you have to decide how much coverage you need (i.e. do you have a garage for rain storms). I know with my brother's JKU the tonneau didn't cover all the way to the top of the rear doors, I don't know if they updated the design at all, but I would guess some rain will find it's way in.
iPhone app user; excuse typos...thanx.