Open source tools to run a CA / PKI have existed for a good long time, they just haven't been easy to use.
Automated certificate issuance software has also existed for awhile, but it hasn't been terribly awesome.
The bigger issue is trust - launching a new CA is quite expensive since you need to invest and build all the technology and processes, then get them all audited, and then present the results to the various organizations who control who control which CAs are trusted (see https://cabforum.org/)
The motivation for running a CA has typically been financial - even vendors that provide free certificates (StartSSL, Comodo, etc) have done so as path to moving customers to paid services.
Lets Encrypt/ISRG was kicked off by a group of folks who care deeply about security and had the technical chops and inside knowledge (some (all?) of the founding team) were from Mozilla and had both guidance and experience dealing with the CAB.
In short, there is no good reason not to have done this, and independent of this, another team within Mozilla had started to think about how we could tackle this before we found out the LE work was in flight :)