For what it's worth, I'm working on a project that calls for a Pi to output MIDI. Just tried it today. I expected it to be more difficult, but I happened to have an interface (Edirol UM-1) that works natively with ALSA, and playing a file out to the synth is as simple as using the "aplaymidi" command (which I am doing from a Python script).
I'm not familiar with any sequencing applications on Linux (perhaps Rosegarden?), but in a live setting, if your sound is coming from synths/samplers, a Pi + some scripts/macros could be a pretty potent tool.
You can use JACK without killing Pulse, but by temporarily suspending it, or routing pulse audio through jack. The JACK FAQ describes the available methods. Jack supports midi out of the box.
Once you have JACK running, you can simply use Qjackctl to route the audio between any jack-enabled software as you want. For example, from your midi controller to Rosegarden to ZynAddSubFX then to your output device.
Because JACK uses shared memory, it can offer very low latency that you won't get with Pulse, particularly as you add any extra applications into the pipeline.
An interesting note is that Wine is also JACK enabled - so you can use windows specific applications in conjunction with your linux based ones - for example, I use Rosegarden together with NI Akoustic Piano, which is windows only software. Unfortunately, VM solutions like VirtualBox don't support JACK, so you'll be out of luck if a piece of software won't work with Wine.
So I'm gonna be that guy and say you can do it for free with Linux...
I currently use Rosegarden running on Ubuntu studio and a midi to usb cable like you mentioned.
With my setup I get full midi notation sent to Rosegarden, I can then playback to my Roland module or playback through sound card using samples.
It all works really well and wasn't very difficult to configure. If you've got a spare usb flash drive and a couple of hours to spare you can create a live boot disk and try it out without making any changes to your current system.
Note: I realise switching to Linux isn't necessarily practical for everyone/every situation, just thought I'd mention a totally free solid option.
Currently my musician uses Musagi, but we're considering moving away from it since the UI is so obtuse at times. Our current other candidates are Musecore, which seems to focus on manipulating the actual score, and Rosegarden, which seems to work on both score and more tech-y synth setup.
I think you can achieve that with ardour and rosegarden (http://www.rosegardenmusic.com/) with Jack you can route the output of rose garden to ardour to record as tracks that you can then record other tracks along side.
You may want to consider giving Rosegarden a try, it is completely free/legal and may suite many if not all your needs. If you are new to linux, I would suggest reading up a little, getting an older spare computer and installing Ubuntu on it. Rosegarden can be installed directly from Ubuntu's package manager.
If your Dad hasn't had any luck finding a cheap copy of Sonar, have you tried Rosegarden? It's free and open-source. It might fit your dad's needs, and is more focused toward MIDI. Sonar can still do it as well - it's more of a jack-of-all-trades - but it depends on what he needs to do.
By the way, plugins are not necessarily resource-intensive, though they certainly can be, particularly complex synths or huge samplers.
This is the one I'm familiar with: http://www.rosegardenmusic.com/
Free, open source. There's no official windows port, but if you're on windows google seems to suggest there are several unofficial ones.
I think the interface you'd be looking for as a non-music person would be the piano-based one. Does require that you know a little bit about a piano, and about how chords and such work, but it's at least better than trying to write stuff out in musical notation.
Cheers!
I might have to do that at some point then. I'm writing this for windows people, because that's what the laptop I'm using is on and the system I have it set up on at the moment.
However, I have an old desktop at home which is my linux box. It also has a proper sound card. Eventually I'm going to have all of this set up on the desktop instead of the laptop, so I could write down steps as I go.
You could have a look around for a pianoteq equivalent if you can't be bothered to wait. Rosegarden seems to be a good option. The rest of what grimborg posted would then apply for tweaks etc.
I'll be writing about VST plugins and soundfonts which seem to be quite cross-platform, so I think that part of my guide will apply for anyone.
I'm not sure if that's possible but there is an alternative to FL studio called Linux MultiMedia Studio that I think is pretty similar to FL studio. http://lmms.sourceforge.net/ or rosegarden: http://www.rosegardenmusic.com/