The inline 6 should be inherently smoother than a V6. Structurally, the inline 6 has less moving parts and a simpler design. In terms of production cost, although the V6 has fewer main bearings, it has more valve gears - which is getting more and more costly these days, with the introduction of twin-cam, hydraulic tappets / finger follower and variable valve timing. Inline 6 is going to be cheaper than equivalent V6. Also, a V6 with a 60-degree angle between cylinder banks is less smooth and a V6 with a 90-degree angle is inherently unbalanced. Okay, the inline 6 has a weaker block and crankshaft due to its length, uneven cooling, and harder breathing than a V6. But a V6 does not have good secondary balance, and therefore needs countershafts to make up for its more complex, and more vibration than straight-6.
Ergonomically, the inline 6 takes quite a bit more space that the V6. Hence the latter is easier to be located further back for better weight distribution. V6 makes very efficient usage of space - which means less weight but inherently worse cooling capacity. V6 also has more energy loss because it duplicates valve gears and camshafts (which increase frictional loss). Because the rods in a V6 are pushing in different directions, these engines are generally rough-revving. They will produce more noise and vibration under throttle. Longitudinal mounted inline 6 doesn’t have space problems, but it engages too much space in north-south direction, thus engage some space which would have contributed to cockpit room.