Here's my two pennies. In my opinion, vector art tools do not lend themselves to pixel art production. I've got Grafx2 (It's like stepping back in time!), Aseprite and a really old copy of Photoshop. When pixels rule, vectors struggle. Each one of these programs has its strengths and weaknesses, but I think you need to devote some time to finding a pixel art program that you feel comfortable with. Or hire somebody!

Pixel art is extremely difficult. I'm no good, and I just dialled it in for Escape From Dinosaur Island DX (the loading screen isn't mine), using multipaint (which doesn't have the features you are looking for).

The following website might be a good place to start. It seems to have layers. Not sure if re-colouring is easy or hard (never used this). Others can certainly help you better. I think 

https://www.pixilart.com/draw

If you want to spend money, I hear that aesprite is quite nice. There is a trial version, if you are not sure (can't save from the trial version.

https://www.aseprite.org/

I spent over two days trying to do the image for the first room alone. I got fed up with it, did the other images and come back to it later. I was originally thinking of doing black-outlined, cartoon-style images, but that turned out to be harder than I thought. I preferred the solid-filled silhouette-style images anyway, but I couldn't get them looking nice. In the end, I chose a photo-realistic style. I restricted myself to a 16-colour palette for each image. The end result looks very much like digitised photos, but you can rest assured that there is a hell of a lot of different techniques involved to get the final result, including very careful photo selection, photo montage, vector graphics, outline tracing, bit-mapped image filters and so on. The end result looks okay, but I'd still prefer the silhouette-style. Most of the work was done with Fireworks, as I've been using that for years. Fireworks has a long history. I bought it when it was owned by Macromedia, then it was bought by Adobe, then Adobe ditched it. Yeah, thanks Adobe. There's nothing equivalent to it on the market and they go and ditch it in favour of their own more expensive products that are aimed at a completely different market.

The only real problems with Fireworks is that there are no brushes that allow you to do airbrush or spray effects without applying transparency and it doesn't seem possible to scale bit-mapped images without introducing anti-aliasing and transparency where you don't want them. Scaling vector images is no problem. (Fireworks does both vector and bit-mapped images.)

Another tool I found very useful was Pixelator. This allowed me to pixelate a bit-mapped image and reduce the number of colours in the palette. This doesn't always work well, but if you can define your palette first and force it to use your palette, the results are pretty good.

To answer my own question that started this thread, I found a program called PixelMash that looks pretty good. It's fairly new and has mixed reviews. People either love it or hate it, but those that hate it were using an early version. Does anyone have any experience with PixelMash? Unfortunately, it's not free (it costs US$25) and you only get a seven-day trial, so I want to do the trial when I have seven days to spare.

Anyway, the graphics are all finished now (unless I decide to change them again). I've loaded a couple of images on the graphics thread. Let me know what you think.