Leaving aside the argument as to whether patents should be allowed, the current system presents large companies like IBM with the following proposition:
Apply and try, succeed: an asset is acquired
Apply and try, fail: an asset is not acquired
For a company like IBM, the cost of filing is negligible. Once any patent is acquired, no matter how illegitimate, IBM can use the patent as a weapon to stifle competition by tying them up in court. For IBM, applying for any patent is all upside if there is any chance at all of bamboozling the patent office into granting the patent.
The patent system, especially as regards software, is irretrievably broken. However, as long as we have it, we need to somehow to create penalties for failed patents that discourage the huge patent holders. Existing cartels of patent holders can squash competitors with their massive joint patent holdings, whether or not the patents could withstand a proper review and legal challenge.
The patent system effectively rewards big companies for filing patents, regardless of merit. Their worst-case scenario is they don't get granted the patent and that has a trivial downside for them.
For the record, I think both patents and copyrights should be abolished. On the copyright side, I went to look up an article on biological populations just a few minutes ago. Springer-Verlag wanted to charge me $39.95 to read it. Assuming for a moment that reading the article has that much genuine value, it means that trillions of dollars of value would be released overnight if we abolished copyrights. Meantime, I declined to pay the $39.95, so information that might have traveled on from there got stopped dead in its tracks.