To be fair to Cisco and maybe I'm way off here. But it seems they do come out with a way to do things first which then become a standard that
they have to follow.
ISL/DOT1Q
HSRP/VRRP
etherchannel/LACP
Yes, and then they keep their proprietary implementation instead of
phasing it out, and no one migrates to the standard one which leads to
vendor lockin.
From my experience - A key thing to consider from any vendor is their
support - Cisco has great support and a large support organization. I've
seen them turn around complex problems very rapidly for their customers.
Additionally, someone already mentioned investment protection and that Cisco
keeps providing incremental improvements such that older 12000s are still up
and running AND supported.
When making an important purchase, these are among the top IMHO.
HTH....
For ISL, I know they are trying to phase that out. For the exams, they are based on dot1q.....
Even if I had all cisco equipment, I'd try to go with standards because you never know down the road where you may
need to use another vendor.
I wouldn't use EIGRP if given a choice, I'd go with OSPF or RIPv2.
Which new Cisco gear has ISL support that you are using?
And in case you haven't read any documentation or spoke to anyone over there in the last 5 years, Cisco pushes dot1q and lacp extensively.
tv
The main problem with this is RIP sucks and there aren't a lot of people out there that are really good with OSPF. For every one legit design and implementation of OSPF, I've seen 50 with every thing in 0 and config statements everywhere.
For companies that don't have real dedicated networking people, EIGRP is much more easy to admin and troubleshoot.
tv
Grrr, IS-IS. SP protocol of choice. Don't believe me, look at some juniper licensing (you'll need to pay us more for IS-IS, but OSPF is available on this cheap enterprise switch for freeeeeeee). Has an annoyance factor of not every vendor supporting it, but lack of IS-IS or some of it's features often shows the caliber of gear you are dealing with or it's current maturity (Brocade MLX had IS-IS v6 support, but didn't support multitopology when I last tested, which gives me an idea of their v6 support compared to vendors such as C/J).
OT: Learned my first hard lesson on playing with routing protocols on production network in non-standard ways. MLX was interconnected using single topology to the cisco which was using multitopology. I didn't expect the v6 side to work naturally. Upon upgrading the MLX to a later code, the Juniper isolated by 2 cisco's from the MLX core dumped the routing process repeatedly. Unplugged the MLX, the Juniper stabilized. Gotta love them nasty bugs. Of course, I suspect the bug was related to interconnecting a single topology into a multi-topology, which you really aren't supposed to do. 
Jack