I have none of them in my 'collection', so my opinion is strictly based on pictures.
Both engines are very well designed, dare I say, even better than the EN (?!). They actually look like a real engine, where the EN (as well as the hobby train) don't come close enough to the original.
The super chief was the beginning of a new era for trains and even though it did not use any special (new) colors, it does not harm the model in any way. But what, I think, is even more important than a great loc, is the availability (through TLC) of nice carriages, something the BNSF engine did not have (exept for the TTX cars). The 'bad' thing about the SC is the fact that it doesn't look good with other (older) TLC cars attached behind it, something the BNSF does !
Even though the BNSF engine did not have a lot of rolling stock to add, it still is a great creation. Nice new bricks and/or colors and I must say, it lookes better in 6 wide than does the SC. The blocky appearance it has is not the result of bad designing, it is the opposite of it. Doesn't the real thing look just as 'square'... (?)
So, if I would have to choose an american (!!!!) passanger train, it would have to be the super chief. The only downside maybe was (and now certainly is) the price you'd have to pay for a train (engine + 2 or 3 cars), but still, 120$ (at the time, with 80$ added if you would like tracks, trafo and motor)) was good value for money. The BNSF engine is a great cargo engine, and can be combined with a lot of (older) cargo cars.