osu78, to answer your question, I chose TD Ameritrade because their $9.99 flat fee doesn't include limits on number of shares in a transaction.
I looked around and most other online brokers that offer lower commissions also charge 0.02 per share over 1,000 or 5,000 shares. Trades of 10K, 50K, or 100K shares will result in a rather large commissions when these per-share fees are added.
The fee structure may have changed with the other brokers since I joined TDA, but TDA is still $9.99 for unlimited number of shares in a trade.
It pays to read the fine print on the commission schedules.