It's not as bad as you think it is.
-RC4 is weak, but the BEAST attack is mostly resolved on clients, and SSLLabs doesn't even penalize you for it anymore.
-TLS1.2 and lack of PFS only really breaks IE at this point, and not the latest version either. In many cases you can sleep at night. Not implementing PFS still doesn't open you up to the major attacks on SSL that are presently out there and will allow IE to work.
-Chain certificate issues are administration problems, and there's no reason not to re-issue your certificates with a stronger signature right now. It doesn't affect clients.
-Not entirely sure about FREAK but from my understanding is the downgrade attack drops you back to export only ciphers which really should be restricted for use anyway. I don't think a default installation of Apache / OpenSSL will make you vulnerable to this downgrade attack as I hope the weak ciphers are rejected. I'm still digging up more info about it.
-OpenSSL supports TLS1.2 just fine and has for a while now.
-LibreSSL isn't available in mainstream distros true, but I would caution against jumping on the bandwagon until the code has been properly re-factored tested and shown to be reliable. The old, never buy version 1.0 of a product rule applies here.
If you abandon older versions of IE you can get an A+ rating on SSLLabs and support all other major browsers. Also again based on my limited understanding that you can specify a cipher order so just because you support IE doesn't mean you don't get PFS and TLS1.2 with a browser that supports it. That only affects clients that connect in an obsolete way. Some of those clients have other internet breaking features like the inability to support virtual hosts with SSL. The only other problem then is a downgrade attack, and even then you can only downgrade to a certain point and if the server doesn't accept vulnerable ciphers then even with the attack you're not in too bad of a shape.
This is just my understanding of the issues. Please correct me if any of this is wrong, I'm by no means an expert on this.