I have no idea what flaked rye would do, I have never used it. I can only imagine it would be even gummier than regular rye in the mash tun and possibly cause a stuck mash.
I used Cascade in this because I thought the citrus notes of it would compliment the juniper. If you want the juniper to really stand out I would suggest you use some of your german/noble hops. They are more subtle and would prevent you from having to store the beer as long waiting for the hops to mellow out. Unfortunately I don't think any of these beers lasted much over a year in the bottle but the last one I drank didn't seem to have drastically changed so I would say no, the juniper and rye most likely will not come through much more with aging.
On a separate note: I recently made a Juniper Porter by using crushed juniper berries in the secondary. It was experimental so I only used 2 gallons of porter. I crushed 3/8oz of juniper berries, I let those sit for one week and didn't notice them much. Let it go for 3 more weeks and still didn't notice much. Let that go for two more weeks and good lord was there a lot of juniper going on! Too much for my tastes. If you decide to "dryhop" with juniper make sure you taste it frequently to get the right amount, I was surprised how quickly that snuck up in the end.