Yes he is linear and is therefore somewhat less valuable as you level him and luck rares up.

Yes, Ratch and Alf are by definition better, and yes Jym is better by proxy.

HOWEVER

if you take a look at this handy table of values I snatched from /u/Zephyron1237... would you like to know where our good doctor sits?

^{small note this assumes you aren't straight up buying copies of cards and only compares the science cost to upgrade them. see reasoning below.}

And guess what? Mega Tron is about the same value as Dr. Shortstack, if not worse. Mega Tron is about halfway, geometrically speaking, between Dr. Shortstack and Ratch in the late-game. He is twice as good as Shortstack and half as good as Ratch.

For reference, Ratch is around 5 times as good as Dr. Shortstack ^{level two used for comparison here,} and Alf (and by proxy Jim) is exactly twice as good as Ratch.

So yes, Dr. Shortstack is bottom tier, but here are two surprising but mathematically accurate things that are less valuable, if slightly, than upgrading Dr. Shortstack to level 2 (assuming you got both Dr. Shortstacks for free).

1. Upgrading 5 commons to level 7 from 6. (note: this holds true while you have at least 26 generators)

2. Buying 5 copies of Alf and then upgrading Alf to level 3. (220,000 science. If Alf is worth ~10x more than Shortstack, 220,000/10 = 22,000 versus the 20,000 to upgrade Shortstack)

And if you don't believe me, here's the formula I used to calculate Dr. Shortstack's worth compared to the others.

relativeValueOfShortstack = newCrit/baseCrit
relativeValueOfRatch = 2
relativeValueOfAlf = 4
valueComparison = log2(relativeValueOne)/log2(relativeValueTwo)
relativeValueMT = 10 ^ averageNumberOfIndustriesWithConcurrentUptime
valueComparisonWithMegaTron = numberOfGenerators * log2(relativeValueOne)/log2(relativeValueMT)

• - level that Dr. Shortstack is going to. Cross reference with first table to see what level Luck rares (i.e. The Confectioners) are (and add 1 for the row that doesn't exist)

averageNumberOfIndustriesWithUptime - uptime for an industry is here defined as 'the time between when you are first able to buy the second of a given generator and when you are producing at least 10 times/second more of both the previous generator (i.e. farmers for communes) and the resource than comrades' because outside of this time Mega Tron is doing nothing. Thus, if you buy your second tank an hour into a 24 hour run and never comrade lock, and buy your second blood-bank 23 hours in, while comrade-locking immediately and, essentially, for the entire time in the other three industries, the value of this variable would be just over 1.

But seriously. That caps out at log2(10⁵ )~=16.6. The worst case Shortstack (not pictured in the table because who tf has level 11 luck chance rares and level 4 w/ max copies Shortstack) is log2(84/76)~=0.144 which makes them even with 115 generators, putting the best case MT vs. worst case Shortstack at a measly 4x value for my lowly level 38 self. It seems the most realistic value for the average number of industries with concurrent uptime is somewhere between 1-1.5 (though perhaps a high ranking player can weigh in on this more heavily), which - when compared to worst-case Shortstack would make Shortstack better between 23 and 34.5 generators, depending on where you wanna place that uptime value.

tl;dr- Yeah, it sucks to get a Dr. Shortstack instead of an Alf/Jym, but he is nowhere near as bad as this subreddit circlejerks about him being.

Also Mega Tron is not as good as people seem to think he is. With best-case assumptions, he's slightly worse than Ratchemus. Realistically he's probably slightly worse than Dr. Shortstack. Dr. Shortstack x 5 ~= MT x 2.5 ~= Ratch

Edit: Is it ever worth buying Shortstack for 40k science?
Is it your first? Maybe
Is it your second? Probably not, but potentially.
Is it your third-sixth? No. Unless you've already maxed out Alf/Jym and potentially Ratch as well.
Is it your seventh? Probably not, but potentially.
Is it your eighth ? No. Unless you've already maxed out Alf/Jym and potentially Ratch as well.

Edit 2: Updated values of MT based on anecdotal example of someone from end-game