ogaugeguy, I think the main difference other than size, is the level of detail. Scale cars are also wider than traditionally sized cars. For example, consider the Lionel scale milk cars: They are based on a smaller prototype car, yet compare a traditional woodside reefer versus a scale milk car and the differences become obvious.
Or the former Crown Model cars, picked up by Weaver: The steel-side box car, the woodside reefer and the outside braced box cars. All three are scale sized, yet based upon a smaller prototype car. They don't look out of place size-wise with traditionally sized trains, but they are more detailed... but not nearly so as the recent Lionel, MTH and Atlas cars.
Or consider the Menards box cars. They are close to scale for a smaller, older prototype box car. Yet on a detail level, they are way more akin to a traditional Lionel type of car. Yet, because of the bargain price, they seem to have appeal to both traditional and scale operators.
I am absolutely a traditional 027 hi-railer. I have in the past, bought some of the smaller scale cars, thinking that size-wise, they wouldn't look too out of place. But it was the higher detail levels that ultimately led me to sell them. I really prefer the "suggested" simplified detail levels, like molded in ladders on box cars.
Also consider that there were a few postwar designed Lionel items that were pretty close to scale proportions, like the GP-9 diesel. Yet if you put a recent production scale detailed GP-9 next to a postwar, MPC or modern-era starter set GP-9, the differences will become quite obvious.
Ultimately this is a question you will have to answer for yourself. You might try viewing a bunch of Lionel train videos on YouTube: I've seen videos showing scale and traditionally sized trains running together. That would be a good way to help you make a decision as to how they look running together. Or going to some train shows with display layouts and taking note of differences between rolling stock items.
