In spite of everything, I think this will be a fine skating event. I hope that everyone does his or her best. If they do (especially Kovtun and Ten

), here’s how it will turn out. Using each skaters’ all-time best score,
Short program
1. Gold, 76.43
2. Medvedeva, 74.58
3. Wagner, 73.16
4. Miyahara, 72.48
5. Radionova, 71.79
6. Hongo, 69.89
7. Daleman, 67.38
8. Tursynbbaeva 61.63
9. Rodeghiero, 6101
1. Jin, 98.45
2. Ten, 97.61
3. Uno 92.99
4. Kovtun, 92.53
5. Voronov, 90.33
6. Brezina, 87.67
7. Brown, 86.48
8. Rippon, 85.72
9. Nguyen, 77.73
Total (top two in each discipline, low placement wins)
Team Asia: 4+6+1+2 = 13
Team Europe: 2+5+4+5 = 16
Team North America: 1+3+7+8 = 19 ...
For the SP comp, the placements of all three men and all three ladies on each team count. Not just the top two.
And the placement points are awarded within each flight.
So the Team Captains

will be strategizing/guessing

as to how best to assign their men and ladies to the three flights.
Emphasis added below.
Day #1 - Friday, April 22 – Men’s and Ladies Singles –Short Program Competition
o Each Team will decide their entries in order of #1-#3 and submit them in closed envelopes ...
o Skaters #1-3 will skate (3 teams) earning points in their flight for their team; Skaters will earn points for first, second or third (i.e. 12, 10, 8 points)...
o Singles Team Short Program Winners will be crowned based on the total team points, an aggregate of the points earned by a team in each flight ...
... Have a certain number qualify directly according to certain rules & then have a "pool" of eligible candidates (also according to rules) from which the the captain's picks can be made.
The TCC rules for qualification did take this two-pronged approach.
Most of the skaters qualified directly:
ISU World Standings on Jan 1 were the basis for invitations for two men, two ladies, both pairs, and both dance couples on each team.
For the third man and third lady on each team, the designated pool of skaters eligible for nominations for fan voting were 2016 Worlds entries.
So your concept already was followed.
If you want to adjust the criteria for direct qualification and for fan voting, that is another story.
For those discussing fraud:
The only "fraud" during the TCC fan voting was automated voting -- automated voting for any skater from any country. (For example: In the Team Europe ladies voting, I do not believe for one second that only one skater received automated votes.)
Like it or not, manual votes -- no matter what the reason behind them -- were not "fraud."
In the real world (unrelated to skating), politics makes strange bedfellows. In some cases, "the enemy of my enemy is my friend." Votes for that kind of reason are not "fraud."