You have a few more problems than some missing tiles. When trenching such as yours, the exposed sides of the old slab should have been drilled and pegged with rebar from one side to the other to help reduce the chance one side will rise or fall different than the other. Was this done in your case? If there is no rebar, the edges of the slab will need to be treated as a cold joint in which case you'd need a grout joint / expansion joint above each side of the trench. Then comes the need to remove more tiles in order to install a crack isolation membrane (or similar) to reduce the chance of in plane movement in the future. This will make for some ugly grout joints. Can I interest you in some nice carpeting?

I had the same dilemna. I have golden oak floors throughout the rest of the house, but I wanted a darker floor in the kitchen. I would have loved an rustic, wide plank wood floor. This floor would not have matched the floors in the rest of the house and I was warned that the transitions from one floor to the other would not look so good by the saddles. In the end, I decided to go with the wood look tile because it works better with radiant heat than wood. I am so glad we did. Between the children and dog it was a good choice for us. I still have to stain the saddles at the two doorways that lead out of the kitchen, but it will be fine. If I used any floor other than golden oak, I would have the transition issue anyway. Love my tile floor! So easy to maintain.

This is just my humble opinion, but a lot of the wood-look porcelain/ceramic tiles that I've seen look better quality than some of the cheapo engineered or laminate "wood" floors out there. And after a year or two, I imagine the quality of the better tiles is even more evident compared worn low-end engineered or laminate flooring. Whether you're talking about tiles or engineered wood, quality makes a huge difference. I love the more unusual looks that wood-look tiles can pull off - looks that would be hard to achieve with real wood like driftwood, etc. For example - That would be a low-maintenance rustic chic look for my busy family lifestyle. When I had ceramic tile in the kitchen, I generally found that wearing "house" flip-flops eased the hardness for my feet. We just extended top-nailed site finished oak planks into our kitchen because we have an open concept living space. Love the look but it was super expensive and I am dreading the fussing at the kids (and myself) that will be required to keep it in decent condition. High traffic areas of the new hardwood were down to bare wood after 12 years before refinishing. I think a lot of flooring looks that are popular now will look dated in a decade - including engineered wood, etc. My grey kitchen tiles weren't too bad, but the 12"x12" shape looked dated after 10 years. So, realistically, plan what will work for you for the next decade, then if you're lucky that your choices work out for longer than that, it's a bonus :) . Here is a link that might be useful: Mission Stone Tile

We are deliberating the same problem.   We have floating floors in the bedrooms. Love the possibility of a quick replace if ever needed.  We have white oak in our downstairs, refinished it 12 years ago.  Still looks stunning.  I put in self stick LVT in our laundry room and upstairs bath.  Looks pretty good. We used EPOXY grout in our kitchen and.bath remodel.  Very LITTLE grout cleaning issues and cracks, and super happy with it. Learned bleaching travertine doesn't harm it and it and now it looks fantastic.  Who would have thought.