Lionel and MTH mix and match

I think it depends on the observer.  I got my son a Lionel El Capitan set, with a FT loco.  I then found MTH F3 dummy A unit and B unit.  He's 10 now and has never noticed the difference, or at least has never said anything in the 3+ years he's had them.  I on the other hand have noticed that the FT is bigger, in other words looks more massive, then the F3s.  Otherwise the striping and colors actually match rather well, IMHO.  But then I'm not a rivet counter type, so I'm not as picky as some can be for these things.

It depends a lot on the particular decoration scheme and how each manufacturer renders colors. In the case of Milwaukee Road, the answer is FORGET IT! Lionel's Milwaukee orange is typically very dark and saturated compared to a prototypical color, while MTH tends to be on the light and under-saturated side. The Lionel orange leans red; the MTH is more toward yellow. Other paint schemes may come out with a better match between Lionel and MTH.

Here is a comparison photo I took of a couple of road switchers - an MTH SD40-2 on the left, a Lionel U-boat on the right. If those colors were on cab units, no way they would look right together. 

With F3/F7s and such it is "going to depend" - I think that is all you can say.  I have  around a dozen ATSF WArbonnet F3s, A and B units, all Lionel or MTH.  Some match better than others, and it is not necessarily MTH vs. Lionel that does not match.  I have some very noticeable color differences among Lionel models not made at  the same time, and mismatches I can notice among some MTH, too, and finally some good matches of MTH and Lionel.  In all cases, though, the b est is a set bought together: an A-B-B-A set, etc.

The photo below shows the worst match I have: the B unit in the middle is MTH Premier and the two end units are a very old Lionel not-quite-scale.  There is a noticeable size mismatch (height), a noticeable difference in the silver (more as to sheen than actual color) and the red on the trim is very red versus almost orange, but the  difference that most disturbs my eye is  in detail: the MTH Premier has screens on the vents, see-through vents on the roof, separately-allied hold rails, etc., and more detail molded into its trucks.  My eye is more uncomfortable with that than the color or even height difference. 

The photo below is of the most recent Legacy E9 and an MTH E8.  They match sooo well it is uncanny, I have to really look to see any difference.  

Finally, if you check my  very recent "Not Daylight Yet: . . . " thread, I posted near the end a photo of how a Williams Shark B unit does not match Lionel Legacy A-A units in B&O livery - not that I thought it would be a perfect match but its about the worst I have ever seen.  I will post later this week what it looks like after some cutting, pasting, and repainting.