I know speed and tackle ability are the prime attributes for players on the kickoff team.

I have tried putting my best guys on the inside, nearest the kicker, and given up TD returns.
I have tried putting my best guys on the outside, farthest away from the kicker, and given up TD returns.

Is there a "best" way to arrange the kickoff team in MFN?

Every time I think I've got it licked, someone busts a big one on me. I have learned from doing big runbacks myself and being a pest:

1. Don't be afraid to put big guys on your kickoff team to distract blockers. Most big disasters happen because the coverage team is overpowered. In RL a returner would simply dance around a big, slow guy, but of course this isn't RL. The conventional wisdom is to avoid guys like that, but the conventional wisdom isn't very wise.

2. Put different kinds of players next to each other to make them harder to block. Lots of owners rely on just one designated playmaker on the coverage team, and if that one guy gets blocked, or if he whiffs, then the coverage team is screwed. I think it's better to take lots of little shots than just one big shot.

It seems to me that your problem comes from putting your best guys all together so that they can get blocked or avoided. Try spacing them out and see it that works better for you.

You're never going to eliminate the threat of a return TD. I typically put strongest (like LBs) in the inside to take on the wedge and fastest on the outside to drive the play to the center.

tasty linebackers...

Your only real defense against kickoff returns is to boot it through the end zone. You can make kickoff returns harder, but you can never solve them completely.

Yep....100 kicking strength (95+, strive for) and narrow the window as much as possible for even having a return.