We have owned two manual Aero convertibles since 2015, and we've loved them both. The first was an '06 and our current is an '07. Honestly, unless you seriously are needing to replace the radio, I wouldn't shy away from the '06s. My wife prefers the newer dash layout, but I really like the '06s.
In 2007, they updated the interior to be more inline with the GM parts bin, which for most is an upgrade. They removed the fiber optic cabling from the head unit, meaning it's possible to replace the factory one with an aftermarket one much easier than before. The driver information center was also moved from by the windshield and integrated into the instrument panel, with the corresponding buttons being relocated to the steering wheel.
2008 saw the front end refreshed, along with the ice block tail lights.
Your main issue is going to be finding that exact combo of v6, convertible and manual transmission. At most, I've only seen 1-2 for sale across the US at a time, so your ability to choose colors will be restricted unless you're willing to wait.
https://www.esaabparts.com/saab/production/data/9-3_2004_2011_CV.php According to to eSaabparts, there were less than 800 made that match your requirements.
From our four years of ownership, the convertibles have been as reliable as the other models. Other than some extra body flex, squeaks and rattles, they seem about the same to me. The issues we've seen are:
1. Coil packs. These are a known weak point on the B284s, and aren't that bad to buy and replace. The Bosch ones are $37 a piece on rock auto. Our old car was still on its factory coils at 108K miles and they were just starting to have random misfires under hard acceleration.
2. Fuel sending unit went out, causing the fuel gauge to bounce around. A Dorman replacement unit was $20, and it cost $300 for a mechanic to drop the tank, or you can do it yourself.
3. P0089. I'm currently dealing with this one now. The code is for low fuel pressure at the rail, which can be one of four parts from what I can tell. The fuel pressure sensor is a five-minute job and is less than $50. There's a fuel pump relay in the passenger foot well that's about $15. A new fuel pump, which seems to be most people's issue, varies depending on what you can get. Factory pumps have been out of stock for awhile, so I'm going to be buying the Spectra replacement on Rock Auto for about $250. Tank has to be dropped, so if you need to take it somewhere, you'll need to factor in the labor. The last part is the fuel pump control unit. If you can find someone with a Tech2, there's a diagnostic it can run to tell you if it's actually the fuel pump or another component.
4. Evap purge valve went out, and can cause two different codes- P0455 or P1455 depending on how bad it's leaking. This can also be caused by a bad fuel cap. Our symptoms were hard starting after refueling and what seemed like a vacuum leak. The part is about $28 and takes less than 30 minutes to replace.
5. Door lock actuators not functioning. From what I've read, you can remove the faulty one and clean it, it's something to do with the contacts inside. I never got around to fixing it on our old car before we lost it, so I don't have a lot of info on the actual fix. I would just end up using the key to unlock the door, as it was an intermittent problem.
6. Peeling dash buttons- I heard this was more of an pre-'07 issue, but our '06 never had any button issues. You can find replacement buttons for the HVAC system online fairly cheap if you have this happening.
7. Top leaking. Our old one lost its waterproofing, so I bought a bottle of fabric top sealant and it was good to go. Our new one leaks like a t-top- around where the weatherstripping meets the window, but only in slow driving or at a stop.
8. Front lip spoiler. Almost everyone that I've seen has been scraped up. Our old one was cracked and scraped from how low it was.
I'm sure others will join in with their experiences, but overall we've loved these cars. Our old one was my wife's favorite car that she's ever owned, so much that she wanted another one when her old one was totaled. She's also convinced me to start looking for a second one so we both can have one.
Not plugging,
https://www.ebay.com/itm/233277173912 but this one on ebay looks nice to me, with really low miles. It's on '07 with the revised dash, and the seller has the original window sticker and everything. Either way, good luck with your search!