Just some observations that might find helpful:
We had a 2.8m Zodiac with an inflatable keel that sat under a wooden removable floor. The idea was to roll it up and store it down one of the quarter berths for our passage from Perth to Cairns across the top of OZ. We couldn't store it on deck as our sloop was barely 25' long and 2' of that was bowsprit.
We ended up inflating and de-inflating it twice before it simply got too hard and we ended up towing it the entire voyage. Attached to a 2-point bridle it was fine apart from once when we had a large following sea and it surfed over the stern and landed in my lap in the cockpit!
When we moved ashore it stayed inflated and we simply stored it under the house when not in use. Yes - a pain loading and unloading it onto the roof racks but not as painful as having to unpack, inflate and assemble every time we wanted to use it.
It was heavy and the keel was prone to coral nicks but it served us well as the wooden floor withstood a fair apart of rough and tumble with anchors, scuba tanks and all the sundry bits and bobs you tend to drop into it.
Our new yacht had a 2.8m Force 4 RIB with an aluminium floor & keel and removable tubes. It went like a rocket and took a hell of a beating without a scratch. No coral nicks, no floor dents - strong and reliable. Like the wooden floored Zodiac I could knock over my fishing tackle box or toss my speargun aboard and be certain I hadn't just turned the floor to swiss cheese. Unfortunately it also weighed a tonne and required a sizable pulley system using the topping lift to haul it aboard. Swings and slides.
Last week we retired the Force 4 due to the age of the tubes and deterioration of the seams as our little dinghy was a good 12 yrs old. We looked at having new tubes manufactured but the costs came out almost on par with buying a new RIB.
We've now purchased a 2.8 RIB with a fibreglass keel and floor. It's half the weight of our original Zodiac and doesn't take the two of us swinging on the topping lift to haul it aboard.
2 pens down from us another vessel purchased an inflatable with an air floor. It also went like a rocket until they accidently dropped their reef anchor onto the floor and punctured it.
I know of a many who also have air floors and have taken the option of installing some light weight, sealed, ply panels for added protection.
As you rightly point out - its always going to be a trade off between storage, assembley, durability and convenience. Me? - the only punctures I want to repair in the future are on our fold-up bikes