This won't necessarily help, but here's a bit of history about how things ended up the way they are today.
The original design for Teensy 3.0 was going to use a 48 pin chip, basically the same physical size as the chip on Teensy 2.0. It had just enough I/O to fill up the 28 pins on the outside edges of the board, 24 signals and 4 power/ground pins.
I first heard about Freescale's 32 bit ARM chips in 2010 and got a some samples and one of their tower boards with the early (larger, too expensive) version of the part. Freescale was about 1 year behind their original schedule for releasing the smaller, lower cost version of chip (in physical packages that could fit on a Teensy board). Samples in 64 pin became available in Jan-Feb 2012. In late 2011 and early 2012, I contacted the Freescale rep and distributors several times, until _finally_ in April 2012 they at least had the part number set up. PJRC placed an order for thousands of chips. I called once a month, to confirm the order was on schedule.
The day before the chips were supposed to ship, Freescale rescheduled with another lengthy delay! I don't recall now if that was while we had the Kickstarter officially launched, or just about to start. It was looking like we'd have to wait another 2-3 months.
However, the 64 pin version was not being delayed. At first, it seemed impossible to fit the 64 pin version on the PCB. But after few days of PCB layout, I managed to just barely make it fit. The bigger chip had a dozen more I/O pins. It seemed like a terrible shame to not be able to bring them out to pins, like so many of the extra signals on Arduino Mega and Arduino Due that can't be used. Adding the pads on the bottom of the board made the PCB layout a LOT harder. At first it seemed impossible, since they block so much area for vias. But after about a week of PCB layout work, I managed to make it fit. All but 1 analog-only pin was at least accessible.
I had considered making the board larger and bringing all the pins to the edges. Perhaps Teensy 3.0 would have been just as successful in a 40 pin format like Teensy++ 2.0? There's always a lot of trade-off decisions in any design, and very strong feedback from a LOT of people involved the physical size., where Teensy 2.0 could fit into lots of projects where Teensy++ 2.0 was physically too big. Even 28 was a small increase over 24 on Teensy 2.0.
Among the many lessons learned from Teensy 2.0 involved the importance of following certain pinout conventions from Arduino Uno. Having at least 14 digital-only pins, Serial1 on pins 0 & 1, SPI on pins 10-13, the LED on 13, PWM on 3, 5, 6, and I2C on A4 & A5 makes so many existing examples "just work" when people follow their hard-coded (either code or documentation) pin specs.
The decision was kept at a 28 pin outside size (24 I/O, 4 power), with 5 power/reset pins on the non-USB edge.
The bottom-side pads were never meant to make Teensy 3.0 "pluggable" in a socket. In fact, they were originally never meant to be there at all. It was truly a last-minute decision to switch to the 64 pin chip, only because Freescale had delayed the smaller 48 pin chip that fit nicely. Basically, the idea is "at least provide some way to get to all those extra pins". Most other boards with high pin count chips, like Arduino Mega and Due, just leave the extra pins unconnected and you can't get to them.
By mid-2013, Teensy 3.0 was becoming pretty successful, with nearly all Arduino functionality working, most libraries ported, and OctoWS2811. But I heard quite a bit of feedback on the limitations of the chip. Even though no other Arduino compatible boards were offering anything close to 16K of RAM at $20 retail, RAM was becoming a huge limitation for a lot of projects. With the audio library planned, more RAM would be needed for effects like chorus and reverb, or projects using audio and many-LED display like OctoWS2811.
From the beginning Freescale has been much better to work with than Atmel ever was. As Arduino became a bigger deal in 2013, they seemed to take some interest. We had been buying the chip in respectable quantity, probably still peanuts for such a large corporation. When I first talked with them in 2010, nobody had heard of Arduino. By 2013, Arduino had become a household name and they were interested in PJRC's efforts to bring their chips to Arduino users.
Freescale gave us a good deal on upgrading to the bigger chip that's now on Teensy 3.1. It still was a pretty good jump in cost, but we agreed to buy more (a bit of a nerve-wracking financial risk for me & Robin....) and we increased the Teensy 3.1 price just a little to try to offset some of that jump. Teensy 3.1 isn't quite as profitable, margin-wise, for PJRC, but overall it seems to have been worth the risk. PJRC has always been first and foremost about projects and publishing free resources.
The new chip was pretty much pin compatible. The only difference was several pins got more functionality. But that 1 analog-only pin I didn't manage to route on Teensy 3.0, because there wasn't anywhere to put another pad (even on the bottom side) and because those 14 rectangular pads block any new vias, now had a DAC function.
True analog output is an awesome feature... far too awesome to leave unrouted to the outside world. Just imagine how upset people would have been with me if I'd taken the easy path of just putting the bigger chip on the same PCB and the silicon had a real DAC that could couldn't get to, at least not without being able to solder a wire to a 0.25 mm pin! I wanted to preserve 3.0 to 3.1 pinout compatibility as much as possible, but the DAC had to come to an outside pin.
I considered replacing A10 or A11. I considered taking away one of the A6-A9 pins. Digital 0-13 and analog A0-A5 are untouchable, since there's an huge universe of Arduino developed code requiring those pins. I thought about removing VBAT. Taking away the place to add a 32 kHz crystal would have made the Teensy 3.1 PCB redesign a LOT easier, since it's right near where that extra DAC pin is.
Ultimately, something had to give, and the reset pin got the axe. Something had to go to make room for DAC output and reset was felt to be the least bad choice.
Luckily, removing reset of the right-edge pad freed up just a little signal routing space on the PCB. I was able to shuffle things around and get that previously impossible-to-route A14 pin to the pad where reset had been, without having to chop any other features. It took a couple solid days of fiddling with lots of traces and vias by less than 1 mil increments, but it worked and passed design rule checks (the PCB is 6 mil spacing, 4 layers, and by far the hardest PCB layout I've ever done).
Moving reset to that little test pad also meant PJRC had to built a whole new bed-of-nails test fixture. There just wasn't any reasonable way to add another pogo pin to the old one. This delayed the Teensy 3.1 release, but in the end I think all this trouble was really worthwhile, to get true DAC output.
Of course, if you're wanting reset on an outside pin, or you want a pluggable Teensy3 with more than the output 24 I/O, this long-winded explanation probably doesn't help. There simply are a lot of trade-offs in making any product for such a wide range of people.
Later this year PJRC is planning to add more Teensy3 products. I can't give you specific details yet, but I can tell you they also involve a lot of these difficult design trade-offs. I really, truly do care about making the most awesome products possible. I am willing to go to pretty extreme design effort rather than taking the easiest path. But there's always difficult trade-off decisions to make, and keeping the boards physically small is always a goal at odds with expanding features.
I do get a LOT of input from a huge number of people with widely varying needs and desires. I try to take as much into account as I can. I often don't have time to reply to every message, but I do read them. If you have input on features, I'm always happy to hear it.