On your point #3. Actually, you are incorrect. Profit is revenue - all costs. Whether or not it counts as COGS is only relevant for gross margin, a metric which isn't the best to judge software companies. R&D is an expense, so it affects your profitability and your net margin. If your company spends $100 less, that's $100 more you have in the bank, $100 less that you need to sell people on.

http://www.investopedia.com/terms/g/grossmargin.asp http://www.investopedia.com/terms/n/net_margin.asp