Don't sell yourself shortThe first thing to remember when designing an realistic alien species is that humanity should either be pretty average, or you should intentionally decide that humanity is above or below average for intelligent species. Why is this? because evolution is efficient! If improving an attribute is possible and actually beneficial, evolution tends to do it. Aliens should have drawbacks for their strengths.
There is also a meta-gaming reason to keep all of these things low: Players have to live with them. Or rather: players pay the same amount for all features regardless of whether they are actually that useful for the character or not. The alien scientist has to find some way to pay for his nose and prehensile tail. Why not pay in the racial template rather than taking it out of the scientific abilities or already meagre combat abilities? The lower the template cost, the more accessible it is to various character types.
Don't just count the arms!One of the most expensive builds known to gurps is the tentacle build. You know, building an octopus with 8 arms. It costs a whopping 100 points to by 6 arms and then upgrade all 8 to extra flexible! But is that really what an octupus should buy? With gurps its important to buy the effects rather than the name. What does extra arm actually buy you?
Well, it gets you a 'hand' and a +2 to grappling. 'Hands' are measured comparative to human hands. So ask yourself, can an octopus use all eight arms as effectively as an human with eight arms? can it play two key boards at once while pulling organ stops, turning the page, drinking coffee, and waving hello? No. And its not just the effects of ham fisted. Its the fact that humans have fingers and opposable thumbs. To some aliens, we have 10 'arms' very short ones on the end of a stump. a LOT of multi-limbed aliens can't use one limb for each hand -- to do what a human does, they need to double up or use some other leverage trick.
Its worth noting extra flexible is often paired with short. Realistic hydrostatic limbs don't have the leverage that a human arm does. Take an elephant for example. Yes, the trunk is huge and fairly long, but so is the animal, and the trunk is used fairly close to the body, especially when its full strength is used. It doesn't have much swinging strength either. Octopi are the same way.
So our the 100 points we spent for 6 extra arms (flexible) and 2 flexible arms don't describe an octopus. They describe a grappling demon with intricate control and digits on the tentacles and immense arm strength. Our actual octopus as two extra arms (flexible, short) and two flexible, short arms for a total of 20 points. And that's just one way to do it. A case can be made for a single arm. Remember, you get what you pay for...
Balancing SensesAnimals generally have the senses they need and nothing else. Humans evolved from animals with sharp senses of smell and hearing, but we currently lack these. Why? because they are not our primary sense. In a similar fashion, other creatures with good senses will usually have worse sight than humans.
Sometimes decreasing sight can seem difficult. a couple of advantages to remember are color blind and non-iconographic. A species that relies on something other than sight could very well have both of them. I also recommend house ruling in the following modifiers for non-iconographic:
complete: You cannot identify anything by sight, other than perhaps a vague shape. you cannot distinguish between faces or read emotions. Your sight is limited to the detection of an object and analysis by general shape. +100%
visual: Your non-iconography is limited to visual input. You can learn the forbidden skills, but only in a non-visual manner: you could learn to read a map based on touch for example. -50%
This may seem extreme and debilitating. It is -- if the alien does not have a culture that has already worked out all of the ways around it using their own superior senses.
Core attributesOne of the most tempting things to do when building aliens is to mess with their basic attributes: DX, and IQ. This is dangerous for a few reasons. It often gives unrealistic results. IQ is so broad that increasing it across the board for a species gives it a huge advantage everywhere. The same is less true for DX, but the point stands. The second issue is that such an approach is bland and is a large use of points for very little differentiation. If I build a scientist with species DX, I'm just going to average out the DX by not buying it raw and going with the species default. If I instead have perfect balance, I end up with a lower DX scientist who is unusually good at balancing.
What are you thinking of when you claim that an alien species is 'smarter'? Are they better at science (use versatile or an academic talent). Perhaps they are superior with social interaction (there are several talents that work -- choose carefully). If their mind simply has a 'higher quality' about it, this is probably just plain will. Or perhaps they seem smarter because they notice more -- thats perception.
High DX? really? that's all you can come up with? Other options can provide more flavour, notably high basic speed (but be careful here) for faster reflexes, and a talent for 'raw athleticism'. If they are actually better at combat, ask yourself if they are better at all combat. Or is it just hand to hand? you can do that with talents too.
Discounting 'equipment' and other 'setting irrelevant' advantagesSome times the super pricey stuff is not worth squat in the setting. For example, age-related advantages. For the most part, people will never see these. The solution is to figure out what they are worth: perk, quirk, feature, usual background, or translated advantage. Most weapons and DR can be represented with a combination of two perks: accessory (the item), and legal immunity (can carry item in public). This should NOT be viewed as an excuse for the player to go hog wild on DR. GM's build templates, and they should look at what the 'equipment' should naturally be and assign that number. If the equipment is truly impressive and stacks with existing tech, an unusual background is appropriate. For example, a race of insects should probably only pay a accessory perk for their DR 2 exoskeleton, but the warrior caste of the same species may have to pay a 5-point unusual background and a legal immunity (armoured in public) perk for their DR 10 carapace.
The 'Translated Advantage' is when only a small part of an advantage is relevant to a campaign. The classic book example is Unaging and 'immune to aging effects' . This can apply to other advantages.