Timber,
For me, I like the plants just as much as the fish, but from what I've heard and seen, koi don't do well with plants. I know you can put rocks around your pots and even use wire to keep them from destroying the plants, but it seems that sooner or later, they will destroy them. If you decide to put some shelfs in, remember the height of your pots. Having a shelf that's a foot deep isn't going to be very good if your using one gallon pots and they are a foot tall.
As for pots, I've found that those square plastic storage tubs work allot better than any of the ones they sell at the pond supply stores. I found that the roots will grow out of those mess sided pots and grow into anything and everythign else. I had to go pull them out of a clients very small pond one time. It was a huge nightmare because they had all grown together. The tubs some people put in there sink for washing dishes works really well too.
The advantages to the sqaure tubs is they fit together real good in the pond. They are bigger than the fish store pots and will alloy more plants or healthier plants to grow. And most important, you can pick them up a year later, or whenever you need to thing them out. They have handles on either end!!!!
If you're set on koi, than plants are just going to be a problem. But if you just want an ornamental pond with fish in it, than common gold fish are great. They will grow to over a foot long if there is enough space for them, they cost almost nothing, and if a racoon eats one or two, your not out very much. They also reproduce like crazy and it's not all that bad to have a few eaten by the local wildlife.
Koi also require better water quality than gold fish. More oxygen and they are more likely to get parasites or sick. That means more hours running the pump and checking water PH. Of course, with the new pool, it won't be that much more to check the water in both of them at the same time.
The thing I enjoy the most about building an ornamental pond is arranging the rocks for the waterfall. Getting it just right is a work of art. A little angle one way or another can make all the difference.
Did you mention lighting? I found that a few spotlights on the waterfall at night time realy adds to the beauty of it. I'd even go so far as to say it's a must have feature!!! hahaha
Eddie