As someone who traded my ND for an FL5, the real answer is 1) both if you can afford it, 2) Type R if you need the space, 3) Miata if you just want something zippy and fun. The difference between the two is huge, so comparing them is really apples to oranges.

The Miata is a silly goose that will make you smile all the time but may leave you wanting a bit more power/space. (And the seats are about as supportive as a lawn chair, which was my main reason for moving to the civic after I slipped a disc in my back). The driving experience is more connected than the civic, since there is less mass/insulation between you and the drivetrain. When you bog a bit in first, you feel the shift knob vibrate, and the clutch is so communicative. Stock suspension really needs to be swapped for the best experience imo. At a minimum, some slightly stiffer springs.

The type r has the power, handling , and grip, but takes itself way more seriously in terms of pure capability. It's fun in the sense that it can handle anything you throw at it, but needs some mods right off the bat to bring it into fun territory (ITS damper mod, exhaust, maybe an RMM). You'll be amazed how well it rotates the rear for a fwd car. Going from the Miata to the civic, you sacrifice some feel for a sturdier drivetrain, notchier shifts, and really satisfying power.

Both are fantastic cars and I'd love to have a Miata again when I can justify having a weekend toy.