While I'm not an attorney I've been involved in numerous IP deals sitting on both sides of the table. One of the biggest misconceptions about patents is many people believe having one is an iron clad wall which will protect them from competition. It just doesn't work that way. I believe that patents are most useful as a negotiating tool used for licensing deals.
The first hurdle in patents is the extent of the claims. Many people try to get them to cover everything they could ever think of doing. The problem with this approach is it's darn hard to prove those claims (e.g. prior art). Instead it's best to keep them tight and well defined to your core business. That way it's much easier to prove and show infringement.
Other companies like to use them as a club to beat down any perceived competition especially after the fact. They like to "stretch" the meaning and intimidate others into sending them money. If you are on the receiving end of this behavior it's best to stand up to them. Most of the time they will back down before going into full scale litigation because they know they can't win. But this is a great opportunity to get them to the table and figure out why they are exhibiting this behavior. Sometimes something good will come of this, but at least you can make them back down.
Years ago we were using a non-Intel chip in a new computer. We knew there was some bad blood between Intel and the chip maker about a potential infringement of one small portion of the chip. So our engineers made sure that portion of the chip was never used. We went to market. Sure enough our attorneys came back to us saying Intel was going to start litigation and we should settle. I stated we had done nothing wrong and if they wanted to litigate that would be just fine, we could pay our expenses from the marketing budget: the publicity would be worth it. The issue died quietly.
So by all means, file those patents, but realize their best use is to promote licensing deals. But if you are being treated unfairly, get the best legal representation you can afford and stop that behavior as quickly as possible. You don't want to get the reputation of being an easy target. And that's in the best interest of your customers and investors.
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