So that's like saying lets give the English and French a bigger chance of winning? Don't think so. There should be the same amount of teams from each country to give an equal chance.
All that merit-based qualification would change is that it would stop the worst teams of the Pro12 like Connacht and Zebre from entering the tournament. It isn't proposed that more English and French teams would take their place. Teams which aren't good enough to finish in the top half of the Pro12 probably aren't good enough to win the Heineken cup, so I don't see it changing the chances of a Pro12 team winning the thing. What it does stop is there being groups with clubs in it which are so understrength compared to the others that the other teams view coming away from games with them without a bonus victory to be a "loss". For example, Pool 3 of the current Heineken Cup has Zebre, Connacht, Harlequins and Biarritz and is a joke of a group. Harlequins will be gutted to have any less than 5-pointers against Zebre and anything less than convincing wins against Connacht. Biarritz will be their only challenge, and the team in that clash which doesn't go through in first place will probably go through as a runner-up. If the group had the likes of Bath and Stade Francais instead of Zebre and Connacht, the group would probably be more competitive and would probably make for better watching.
Sure, Connacht and Zebre lose a bit of money. But the Heineken Cup isn't there to subsidise clubs, it's there to provide the highest quality in European club rugby.
I think the fairest (but admittedly more complicated) way of doing it would be:
Top 6 teams of the Pro12
Top 6 teams of the Premiership
Top 6 teams of the Top14
A: Suppose that two nations are represented in the top 6 of the Pro12. Then from the following list, whichever applies first:
1. The winner of the HEC if they don't get into their domestic top 6.
2a. If a team enters the HEC through 1., then a playoff between the highest ranked of the two other nations not represented in the top 6 of the Pro12.
2b. If a team doesn't enter the HEC through 1., then the highest ranked clubs of the two other nations not represented in the top 6 of the Pro12.
B: Suppose that three nations are represented in the top 6 of the Pro12. Then from the following list, whichever applies first:
1. The winner of the previous HEC if they don't get into their domestic top 6.
2. The highest-ranked club of the nation not represented in the top 6 of the Pro12.
3. The runner-up of the previous HEC if they don't get into their domestic top 6.
4. The winner of the Amlin if they don't get into their domestic top 6.
5. The seventh placed club of the domestic league which the winners of the previous HEC are in.
6. The eighth placed club of the domestic league which the winners of the previous HEC are in.
C: Suppose all four nations are represented in the top 6 of the Pro12. Then two from the following list, whichever applies first:
1. The winner of the previous HEC if they don't get into their domestic top 6.
2. The runner-up of the previous HEC if they don't get into their domestic top 6.
3. The winner of the previous Amlin if they don't get into their domestic top 6.
4. The seventh placed club of the domestic league which the winners of the previous HEC are in.
5. The seventh placed club of the domestic league which the runners-up of the previous HEC are in.
6. The winner of a play-off between the seventh placed teams of the two other leagues.
Gives 20 teams. 5 groups of 4. 5 winners, 3 best runner-ups. Not likely for there to be some woefully inadequate teams. In the unlikely event a play-off needs to be played, it happens a week before the season starts in place of a warm-up friendly.