The issue is that three of your five points don't actually make any difference on the field at the moment. Age, homegrown and ability to play CB (it's a decent option to have but we never really use it). McTominay is stronger, better in the air, and is a decent goal threat for a midfielder. Three things which are definitely nice bonuses to have, but that's all they are - bonuses. I consider the most important job of the midfield is to give the team control of the game (perhaps you feel otherwise), and Scott is fairly average or even poor in pretty much all the important aspects.
- Making themselves available to receive the ball. McTominay is downright poor at this, constantly hiding (I don't think it's deliberate but it has the same result) behind opposition players so that he is impossible to pass to. There's a reason he gets on the ball about 20% less than any of our other three midfielders and sometimes has games where he is basically invisible. He just doesn't provide our players an option to pass to which makes it more difficult for us to build anything. Meanwhile Fred is constantly moving around offering himself as an option.
- Passing. Fred isn't a great passer, and you do touch on a fair criticism that some of his 'completed passes' did actually make it difficult on the recipient. But Fred not only makes more passes, he makes more creative and attacking passes that get us into dangerous positions and creates more chances, makes more longer passes, and he is also more likely to push us forward when we are building the play out from the back. Overall he's attempting to do a lot more with his passes than McTominay does, who (other than the occasional nice diagonal ball to the left wing) tends to play it more safe and basic.
- Setting the tempo. It wasn't as obvious towards the end of the season as Fred was struggling for form, but normally he is very important for us at speeding up the tempo. Without him we constantly look very pedestrian, just playing it around slowly when we have the ball and sitting off and letting the opposition play when they have it. Fred tends to inject that bit of drive and speed particularly defensively, but also trying to play the ball quickly up through the middle of the park to Bruno when he gets into that bit of space between the opposition midfield and defence. Once again I wouldn't necessarily say he's particularly good at the latter, but he's better than Scott.
- Pressing and winning the ball back quickly. This is becoming increasingly important in todays game, with almost all top teams trying to harry the opposition and quickly win the ball back high up the pitch. Obviously Fred is one of the best around at this. Scott does have the occasional game where he does it well (normally in a big game - PSG comes to mind), but otherwise he's surprisingly average/poor. He tends to stand off and let the opposition play to their own tempo too much.
These four aspects, alongside protecting the backline in deeper areas where I'd rate them about the same, are probably the most important things for a midfielder to provide IMO. Think of all the top deeper midfielders over the years and they'll almost all be great at three or four of those five things. Maybe the more limited ones will be absolutely amazing at one or two of them.
McTominay does have the occasional two or three games a year where he does step up and show a lot more. Particularly with (as you mentioned) driving forward with the ball and also playing more attacking passes. It seems like he basically decides in those games to force the issue and make things happen himself. If he starts having those games more regularly than maybe things will change (although he would still definitely need somebody next to him acting as the main playmaker), but for now in the majority of the games he's simply not providing enough. Taking those five important aspects that I listed above, there's none that he's even above average.