Unless the car came with the 250, I'd always look at the 200 first. The 250 (4.1) is much harder to fit. There are severe space limitations on 250 Fords in all unibody Fords. Its a very tall engine that needs a lot of very specialised gear to package it. The gear is around, but it will always be rather expensive.
If your making a killer turbo race car, a 250 is just fine
Generally, the 200/3.3 is the small I6 engine you'll find most often. It has 30 years (1964 to 1984) of service to its name.
The basic 200 cube numbers are hard to beat. The 200 is way lighter by (almost 100 pounds), shallower( by 1.67"), shorter (by an inch or so), narrower (by an inch), and only requires simple, lighter duty axles, gearboxes and four stud suspension parts. It is way cheaper to fit, and if its already there, bolt on mods which take it from 67 rear wheel hp to well over twice that are there to be had.
There is a point of diminishing returns with a 250, because the additional periferal weight of a good gearbox/drive train/axle/suspension/brake combo will take away all the gains. So 25% more capacity doesn't ever give 25% more power on a 250. A better head on a 200 gives it way more power than the same better head and carb does on a 250.
The old addage. For straight line go, go cubic inches or There Is No Substitute for Cubes is not the case when you have a stock 200 with T5 and a 32/36 carb verses a stock 250 with any gearbox and a 2-bbl carb.
A little note. In Australia, circa 1982, the 3.3 5-speed Falcon had a 17.9 second standing quarter and 112 mph, the 4.1 auto had 18 second qaurter miles at 112 mph. A 4-speed 4.1 manual was 17.6 senconds, and 112 mph. The smaller engine gave 27.2 mpg, the bigger one 22.7 mpg. The power gain was insignificant verses the loss of fuel economy, and the bigger engines had a weight penealty (power steering, better brakes, needed).